I've made a table with some statistics for the different nations, based on the area associations in the Scenario handbook. Areas that belongs to more than one nation has been divided between them, and areas belonging to no nations has been split equally between neighboring nations. The adv civ statistics is 8 players with western expansion. Nation statistics is color coded compared to the average on the CivProject map. All green = overpowered; all red = underpowered. Everything else is a matter of interpretation. I haven't had time to analyze this data yet, I'll get back to that later.

	AdvCiv Total	AdvCiv / Player	CivProject Total	CivProject / Player	Minoa	Saba	Celts	Assryia	Rome	Babylon	Carthage	Hellas	Nubia	Dravidia	Parthia	Maurya	Persia	Hatti	Iberia	Indus	Kush	Egypt
City Sites	61	7.63	108	6.00	9	5.5	3.5	5	6	4.5	7	6	6	5.5	5	6.5	4.5	6.5	5	7	7	8.5	City Sites
(0)-pop			15	0.83	0	2	5	0	0	0	1	0	1.5	0	1	1	0	1	0	0	1	1.5	(0)-pop
(1)-pop	57	7.13	142	7.89	7	12.5	10	3	4.5	3	9.5	10	8.5	10.5	8.5	12.83	5.5	6.5	8.5	10.33	5.33	6	(1)-pop
(2)-pop	51	6.38	99	5.50	4	6	6.5	4.5	6.5	5	5.5	4.5	5.5	3	4.83	5	5.5	11	5	4.33	6.33	6	(2)-pop
(3)-pop	29	3.63	38	2.11	2	1	3	6.5	1	3.5	2.5	1	0	2	1	3	3.5	0	2	2	2	2	(3)-pop
(4)-pop	6	0.75	8	0.44	0	0	0.5	1	1	1	0	0.5	0	0	1	1	1	0	0	0	0	1	(4)-pop
(5)-pop	3	0.38	2	0.11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	(5)-pop
Areas	146	18.25	304	16.89	13	21.5	25	15	13	12.5	18.5	16	15.5	15.5	16.33	22.83	15.5	18.5	15.5	17.67	14.67	17.5	Areas
Pop w/o A	285	35.63	496	27.56	21	27.5	34	35.5	24.5	27.5	28	24	19.5	22.5	25.17	35.83	31	28.5	24.5	30	24	33	Pop w/o A
Pop w. A	431	53.88	800	44.44	34	49	59	50.5	37.5	40	46.5	40	35	38	41.5	58.67	46.5	47	40	47.67	38.67	50.5	Pop w. A
Expansion	235	29.38	436	24.22	19	26.5	30	27	21.5	22	25.5	22	19.5	20.5	22.17	30.83	25.5	28.5	22.5	25	22	26	Expansion

I'm now done with the analysis, and has a suggestion for improvement. I've concentrated my efforts on city sites. There is 109 city sites on the map, so that means there should be 6.06 city sites per player on average. I also considered population figures, both with and without agriculture, but here I accepted a 10% error margin.

To avoid "safe corners" appearing when nations isn't in play I decided to go for 5 cities per player, plus two halves, giving a total of 6, close to the average. If two neighbors didn't share a city, I tried to get them to share some pop space instead, to still force some interaction towards the center of play. (In case you don't remember: shared areas is removed even if one of the nations still is in play)

First some corrections and "obvious" changes:
A) Kuhwat wasn't mentioned in the scenario handbook. As all neighboring areas was associated with Kush, I associated it with Kush.
B) Deccan wasn't mentioned in the scenario handbook. As all neighboring areas was associated with Dravidia, I associated it with Dravidia.
B) Damascus was associated with Babylon, even though all neighboring areas was associated with Assyria, so I changed it to Assyria.
C) While Cyprus generally is considered Minoan territory, it doesn't make sense to have it in play if you don't use anything east of Minoa, so I associated it with Hatti as well as Minoa.
D) While Sardinia and Caralis would be a too good safe corner for Rome is Carthage isn't in play, it doesn't make for Carthago to use it if Rome wasn't in play. Additionally, I have so far never seen Carthago use the island of Sardinia, though I have heard him threaten Rome to give him the whole of Sicily, or I'll go take Sardinia instead. In the end I decided to associate Sardinia and Caralis with both Rome and Carthago.

Next, a walk through of my proposed game balance changes:
1) Even though D above, Carthage is still slightly overpowered with a total of 6.5 city sites. Of the three half cities of Carthage, I decided the one that made most sense to give up was Syracuse. While Rome has to many city sites as it, it can give some away in the other end, and Syracuse won't become a safe corner, as it's close to both Hellas and Mina, both of which tend to go city fishing with astronomy.
2) Now Rome has to many cities, but Iberia has to few. This would be balanced by "giving" Iberia half of Masilia, as well as Rome's half of Lugdunum. This small change actually makes Iberia quite balanced, still slightly short of pops pace, but well within my 10% error margin.
3) Rome is also slightly short of pop space. This one is easier to fix though, as you can easily move the Roman/Celtic border one area, giving Rome the whole Cisalpina, and sharing Noricum with the Celts.
4) On the issue of the Celts, they have far to few city sites, but far to much living space. As the opposite is true for Hellas (especially taking it's close proximity with Minoa into consideration) I decided to do a swap. Hellas gets the whole Moesia, while having to share Odessus with the Celts. This brings the Celts up to 4 city sites (2 for himself, 1 shared with Iberia, and 1 shared with Hellas), witch I think is doable, as he has huge pop areas to produce tokens for wilderness cities in.
5) That change brought Hellas below the average 6 cities, so giving him half of Chalcis from Minoa makes sense. This little city forwarding from Minoa to the Celts through Hellas had the additional bonus of getting Hellas to the 5 + 2 halves I talked about above.
6) This leaves Minoa with a respectable 8.5 city sites, but with far to little pop area. Even though getting a boast from the Celts, Hellas has no spare to give Minoa, so instead I go east, taking Ionia and Lycia from the Hatti. This has the advantage of creating a Minoan corridor to the shared Cyprus. This change balances out Hatti quite well, slightly below average on pop, but half a city in surplus. It's not as if any of Hatti's neighbors need that city site anyway. Minoa is still far short of average pop space, but this is just part of the Minoan game style, and is mostly compensated by its extra 2.5 city sites.
7) Jumping down to Saba, I found that it indeed was quit balanced already, half a city site short, but with a decent surplus of pop space. Quite interesting that that the "eastern Crete" as some likes to call Saba (due to the fact that Saba and Minoa usually is among the first nations to get astronomy and cloth making) is more like a mini Celts in population base.
It's neighbor Nubia is however quite underpowered. Fortunately the megaoverpowered Egypt is close by, so I just moved the border north somewhat, giving the shared Teiga, Nukheila and Buhen to Egypt, and instead letting them share Upper Egypt and Ptolemais. Leaving Nubia dead on average. Unfortunately not sharing any city site with neighbors, but as Nubia isn't likely to be played without both Saba and Egypt present that is of minor concern.
9) This still leaves Egypt just over average pop, but with 1.5 city sites to much. Considering the Egyptian floods this should be quite balanced anyway.
10) Now looking at Assyria, also megaoverpowered. Babylon is however below par, so moving the border remedies that problem: Babylon gets Mari, Carrhae and Nineveli, and then Assyria only have 6 city sites and about average pop.
11) The extra boost from Assyria ensures that Babylon can give Persia both Susa and Gerrah, which Persia really needs. This leaves Babylon with slightly above average pop, but due to low area count actually below average when considering agriculture, so quite balanced I think.
12) Persia is still half city site short, but with some pop to spare. Parthia however, is worse of, even with half of Bukhara and Upper Oxus from Kush, Parthia is still half a city short, but without pop to spare, so Persia have to give up his parts of their shared areas (Drangiana, Kavir, and Zagros). This leaves Persia with above pop average without agriculture, but below with, and Parthia the other way around. Quite nice, except they are both half a city short. In absence of one to share, that will have to do however.
13) After having to yield (part of ) some areas to Parthia, Kush is in really Bad shape, but by assigning Aria to Kush, and transferring Sulaiman och Arachosia from Indus, Kush is in decent shape again. Slightly low on pop, but with an extra half a city, that's no big problem.
13) Next problem is Dravidia, that is in severly underpowered, but by giving Nalas and Vidarbah entirely to Dravidia (as opposed to being shared with Maurya) and getting half of Lothal from Indus, and Dravidia is OK. Lowest pop on the eastern third of the map, but still within the margin of error.
14) The last problem is balancing out Maurya and Indus, which I accieved by assigning Matsya to indus, and making them share Avanti.

The resulting statistics is as follows:

	CivProject Total	CivProject / Player	Minoa	Saba	Celts	Assyria	Rome	Babylon	Carthage	Hellas	Nubia	Dravidia	Parthia	Maurya	Persia	Hatti	Iberia	Indus	Kush	Egypt
City Sites	109	6,06	8,5	5,5	4	6	6	6	6	6	6	6	5,5	6	5,5	6,5	6	6	6,5	7	City Sites
Areas	299	16,61	14	22	23	13	15,5	12,5	17	16,5	19	17	18,5	18,5	13,5	16,5	16,5	16	15,5	14,5	Areas
Pop w/o A	489	27,17	22,5	29	28,5	28,5	27,5	31	26,5	27	25,5	24	27,5	28,5	30	25,5	25	27,5	25,5	29,5	Pop w/o A
Pop w. A	788	43,78	36,5	51	51,5	41,5	43	43,5	43,5	43,5	44,5	41	46	47	43,5	42	41,5	43,5	41	44	Pop w. A

The scenario handbook section would thus become:
2.1 Civilization Area Association
2.101 This section details the areas that are associated with every civilization. Simply because an area is considered associated to a civilization does not imply that a civilization has innate sovereign rights to the area. It is simply a term used to associate areas to particular civilizations for the purpose of this Scenario Handbook.
2.102 Some areas are associated with two or more civilization. How to deal with them is addressed within the appropriate sections below.
2.103 Minoa - The following areas are associated with Minoa: Argos, Chalcis, Cyprus, Eretria, Ionia, Knossos, Lemnos, Lesbos, Lycia, Miletus, Peloponnesos, Phaestos, Rhodes, Sparta, and Thera.
2.104 Saba - The following areas are associated with Saba: Aden, Arabia Deserta, Arabia Felix, Azania, Bat, Berbera, Calmadow, Hadhramawt, Himyar, Ma'in, Madrakah, Marib, Nabataea, Nafud, Ogodan, Oman, Opone, Qutaban, Saba, Socotra, Ubar, Yathrib, Zafar, and Zufar.
2.105 Celts – The following areas are associated with Celts: Aleisa, Belgica, Britannia, Caledonia, Dacia, Dyfed, Germania Inferior, Germania Magna, Germania Superior, Getae, Hibernia, Londinium, Lugdunensis, Lugdunum, Lugia, Noricum, Northern Wastes, Odessus, Sarmatia, Scythia, Sudeten, Tomi, Ultima Thule, Upper Danube, and Upper Rhine.
2.106 Assyria - The following areas are associated with Assyria: Aleppo, Antioch, Armenia, Assyria, Caucasus, Cilicia, Damascus, Jericho, Lesser Armenia, Nalchik, Phoenicia, Salamis, Sidon, Syria, Tyre, and Van.
2.107 Rome - The following areas are associated with Rome: Campania, Caralis, Cisalpina, Corsica, Etruria, Illyricum, Massilia, Milazzo, Neapolis, Noricum, Pannonia, Rome, Rubicon, Salonae, Samnium, Sardinia, Syracuse, and Tarentum.
2.108 Babylon - The following areas are associated with Babylon: Babylon, Babylonia, Carrhae, Chaldaea, Charax, Elam, Lesser Armenia, Mari, Media, Mesopotamia, Nafud, Nineveh, Sumeria, and Ur.
2.109 Carthage – The following areas are associated with Carthage: Caralis, Carthage, Cirta, Cyrene, Eastern Getules, Eastern Mauretania, Jalo, Libya, New Africa, Numidia, Panormus, Sabrata, Sahara, Sardinia, Thapsus, Tripoli, Tripolitania, Tunisia, Western Getules, and Western Mauretania.
2.110 Hellas - The following areas are associated with Hellas: Aetolia, Appolionia, Athens, Boeotia, Byzantium, Chalcis, Corinth, Epirus, Illyricum, Ithaca, Macedonia, Moesia, Odessus, Paeonia, Phocis, Thessalonica, Thessaly, and Thrace.
2.111 Maurya - The following areas are associated with Maurya: Assaka, Avanti, Bihar, Brahmaputra, Chedi, Eastern Himalaya, Gauda, Kalinga, Kausambi, Magadha, Malla, Orissa, Panchala, Pataliputra, Rupar, Tamluk, Tosali, Ujjain, Vatsa, and Vidisa.
2.112 Dravidia - The following areas are associated with Dravidia: Anuradhpura, Asmaka, Brahmagiri, Cholas, Deccan, Eastern Ghats, Lothal, Madurai, Nalas, Pandyas, Prathistana, Ruhuuna, Shakas, Sinhalese, Tosali, Vanchi, Western Ghats, and Vidarbha.
2.113 Kush - The following areas are associated with Kush: Abhisara, Arachosia, Aria, Bactra, Bactria, Bukhara, Gandhara, Harappa, Kalibangan, Kuhwat, Kuru, Rupar, Samarkand, Sulaiman, Surasena, Taxila, Upper Oxus, and Western Himalaya.
2.114 Nubia - The following areas are associated with Nubia: Adulis, Ahmar, Aksum, Azania, Bahrmeder, Barbaria, Buhen, Danokil, Meroe, Napata, Nuba, Nubian Desert, Nukheila, Ogodan, Ptolemais, Salima, T'ana, Teiga, Thebes, Upper Egypt, and Upper Nubia.
2.115 Persia - The following areas are associated with Persia: Bat, Carmania, Gedrosia, Gerrah, Harmozia, Liyan, Magan, Maka, Persepolis, Persis, Persua, Sagartia, Susa, and Susiana.
2.116 Hatti -The following areas are associated with Hatti: Alani, Ankara, Bithynia, Cappadocia, Caucasus, Cilicia, Crimea, Cyprus, Galatia, Gordium, Kanesh, Kuban, Maeotia, Mikop, Nalchik, Salamis, Sardes, Sinope, Troy.
2.117 Iberia – The following areas are associated with Iberia: Aquae Sextiae, Aquitania, Baleares, Caesaraugustanus, Carthaginensis, Carthago Nova, Cluniensis, Corduba, Ebusus, Emeritensis, Gallaecia, Iberus, Lugdunensis, Lugdunum, Lusitania, Massilia, Narbo, Western Getules, and Western Mauretania.
2.118 Indus - The following areas are associated with Indus: Avanti, Balakot, Chanhu-Daro, Dholavira, Kalibangan, Lothal, Makran, Maru, Matsya, Mohenjo-Daro, Poura, Sattagydia, Siestian, Sind, Surasena, Surashtra, Thar Desert, and Upper Indus.
2.119 Parthia - The following areas are associated with Parthia: Bukhara, Caspian Coast, Chorasmia, Drangiana, Eastern Parthia, Gorgan, Hecatompylos, Karakum, Kavir, Media, Merv, Nis, Nisa, Paraetacene, Sogdiana, Toprok-Kala, Upper Oxus, Ustiurt, Western Parthia, and Zagros.
2.120 Egypt - The following areas are associated with Egypt: Alexandria, Cyrenaica, Cyrene, Eastern Desert, Fayum, Gaza, Jalo, Jerusalem, Memphis, Petra, Ptolemais, Sinai, Siwa, Tanis, Tyre, Upper Egypt, and Western Desert.

Any comments, corrections, counter proposals, etc?

Sounds good. I noticed you didn't take into account the AST or the secuirty of being on a border though. I'm happy to give it a try next time though!

I did take security of being next to the map edge (I assume that's what you mean with border) into account, that is why I'm trying to make sure to always remove some extra areas at the new map edge (the shared areas), thus forcing the player at the (new) map edge to go to the less secure inland. When I said "force interaction" I mostly meant "force conflict"...

You are right that I mostly ignored AST though. But even if that turns out to be a problem, it should only require minor changes to fix. I'm willing to give it another look after seeing a game with a civilization with an non-standard AST next to a new map edge.

Based on the first GothCon XXXI playtest I'm drawing the conclusion that Egypt has no problems, even though it's reduced area and poor A.S.T. (5 VP loss). Assyria, however, needs at least Ninevehe back, perhaps also Carhae. I'm going to go one area at a time though.

I've also got yet another playtest questioning why the *@#$ Hatti enters the early bronze age one turn earlier than most nations, thus loosing 5 VP. This must be fixed.

Based on the second playtest I'm also drawing the conclusion that the new borders for Persia, when only playing the six easternmost nations, is good.

As for the rest, I'm still waiting on more playtests.

All your proposed changes sound good to me...