Ok. As a result I have some questions. Do you remember 13c. scenario's map. There are 6 sities available to LGD. 5 of them (the territories whish reperesentive) were the part of LGD practically since it was founded. Only Smolensk became the part of it in 1404 and was captured by Muscovy for rather long period. Some people consider it to be the bielorussian sity in Russia (with Bryansk) but there is no chance of returning it to Bielarus. Nevertheless, this map illustates that LGD consists not only of modern Lithuania, but also Bielorussia whish was the part of LGD from very beginning (some of them a bit later) up to Polish-Lithuanian Commonwealth partition between the Russian Empire, Prussia and Austria.
This doesn't suggest anything (EDIT: actually it does suggest it, but what's wrong with it?), this is intentional and by no means limited to Eastern Europe, e.g. if you look at Aragon and Portugal, it's the same. You can see that they start with cities that they technically captured 50-100 years later. The readme/first post of this thread mentions "A compromise between historical accuracy, playability and scale". In this particular case you have to consider game balance and the limitations of Civ3 engine. Unfortunately, unlike in Total War series, we cannot have "independent cities". Therefore the area of Smolensk either has to be excluded, leaving a huge gap on the map, or given to either Lithuania or Vladimir-Suzdal Rus. Vladimir-Suzdal was already too powerful (and they should be weak, much weaker than the Mongols at that time), while LGD took control of Smolensk later, as you have said, so it made sense to give it to LGD. I wish we could have more than 31 players and/or independent cities to include all the principalities of Eastern Europe, but it cannot be done.
But the list of sities available to Lithuania nation is rather strange:
1. 34 modern lithuanian sities/6(7) modern bielorussian sities/1(2) ruthen one. 6 or 7 means some doubts about Braclaw (in Ukraine) (probably it is Braslaw in Bielorussia - I don't understand your choise of Braclaw - where are other ruthenian sities?).
-The population of Bielarus more than 9 millions people. 7-8 of them are the Bielarusian people whose ancestors lived in LGD. The population of modern Lithuania is 3,6 millons inhabitants, but not the whole modern Lithuania was the part of LGD.
So, 34/6(7). It's something strange. I consider it to be 1/3.
2. Then 34 sities... Some of them, for exemple Ignalina was founded by Russia!!! in 1810, Neringa (it is a Curonian sity) became the part of Lithuania in 1920, Shilute became the part of Lithuania also after WWI. They should be deleted from the list.
Two issues here. The accuracy of some of the lists may not be perfect, that is true. There was no Lithuanian (or Russian for that matter) historian that would give us suggestions when the mod was still in development, so we used mainly English and Polish resources, and primarily internet ones, for constructing these city lists. There's also the problem of contradictions in history especially between Russian sources and the West, so to speak

For instance, your example of Ignalina - according to English wikipedia this isn't really a bad entry. You cannot expect me to consult Lithuanian historians just to find if such a town could have existed there in 13c or not

especially since it's not on the map, just a name at the bottom of the list... Those cities that you know for sure that were founded after middle ages I'd remove for sure, but it's a bit late now, as the mod is really done.
That brings another issue. The "34 modern Lithuanian cities" I cannot agree with. Most of these either were medieval Lithuanian cities or their names were used back then (like Memel/Klaipeda), even if the towns belonged to other Baltic tribes before, and German knights after (remember, they are not in the basic mod, and in the 11c version I've given several Baltic sites to not-yet-formed Lithuania, again, it's either that or a gap in the map). For cities like Braclaw I don't see a problem as they were under the influence/control of LGD, same as say, Dutch or French cities that are on the German/HRE city list. Again, this is not about modern Lithuania, ethnic Lithuanians, but the Grand Duchy and all areas it influenced and controlled. I'm not sure what are you suggesting, that the list should be 1/3 of what it is to be 100%-true-Lithuanian? In that case, when playing the game, instead of Klaipeda or Braclaw you'd have a city called "New Kernave" or "New Trakai"...
3. I realise that Lithuania is interesting because of pagans and archaic language... but the official language was written Ruthen (however it is different from spoken language of slavic regions of Lithuania), sometimes Polish or Latin (for the period of these scenario). The Lithuanian languages were the spoken only in some ethnic lithuanian territories which is only a little part of LGD. Some baltic languages were spoken in the modern Bielorussian territories too, but they arenot Lithuanian ones. I want to say that the Lithuanian names of even Lithuanian sities arenot necessary. They were fist mentioned according to slavic phonology (for some in german), offical Lithuanian names were obtained only in XX c.
As for this and your second post, I think you're taking it a bit too seriously, the whole heritage thing and all. Why get languages, or even nationalities, into this at all? These weren't even relevant in the medieval political landscape. That, and this is first and foremost a game. Also, I think we went a bit farther with the depiction of Eastern Europe (especially on this scale, where all Europe and Near East are included) than most mods/games did, even the much better mods for Total War series. For instance, in all games/mods I played, no one really bothered with Ruthenian principalities/kingdoms at all e.g. Galicia-Volhynia.