Hegemonia: You already said it, the city models are unique and very impressive. If we could get that, at least for the likes of Rome, Carthage and Alexandria. The rest was a good, but not stable mod, we should probably find out if there is a connection to either the unique city models or the Persian invasion script.
The Hellenic States: Not going to be disrespectful to comrade_general, but it was still quite close to vanilla. It was decent to see a mod for the early Diadochi wars, with the changed map, factions, characters etc., but I can't remember any really new features.
Invasio Barbarorum: Well, there are different versions here.
Flaggellum Dei makes full use of the horde features and adds great new buildings and units. It's still closer than vanilla than other versions, but it's that improved version of the original
Barbarian Invasion any player would like. Very stable and the Campaign AI never seems to give up, but not really an unique feature here. Then, the mod/series (since they are different campaigns) about
Emperor Julian and his foes. They feature a complicated religion system (you either have to destroy all Pagan or Christian buildings and convert to opress mass riots) and a new camera perspective in battles, which is interesting, but a bit complicated. Other versions are similar, they crash sometimes, but for the great armies and dozens or hundreds of new units it's still pretty stable. Most of the post- Flagellum Dei campaigns are very challenging, maybe too much for the common player. The graphics are greatly improved in the later versions, too.
Rise of Persia: ROP is a very interesting, and the only, attempt to show Total War from the perspective of the Achaemenids. The campaign map is a but unbalanced, especially in the West with too many rebel settlements being overrun by Tarentum and Sparta mainly and Athens seems to be flawed, because in 90 % of the campaigns it neither expands nor loses since it allies with Sparta. ROP has some unique and nice units like the Indian generals, who sit on elephants and have parasols
There is also a script for several turns a year, but you always need to activate that one when loading and I sometimes forgot to. Graphics are not superior, but some units are, as I said, very creative and show some unexpected possibilities.
I completely forgot about their government system, cities can be governed by tyrants, democracies or aristocracies, which brings different levels of public order and happiness. The modders used BI's religion system to implement it- government is initally set by the atrributes of the settlement's governor, unless you build new buildings to change it.