Factions making more money... some maybe but as Epeiros I had all of Greece and Krete + Serdike I believe (abandoned Taras at the start to let Romans expand) and I had a million by 250 so you can do very well if you're not completely surrounded by enemies.

Access to elites at the start... you could do that capitol thing it won't influence the game much giving every capital a L4 MIC

City Mod.. didn't use it too much can't say it could help. Limiting the huge cities could be more historical but it will not solve your army problems because MICs aren't tied to city size so having huge cities by 250 is not bad for the conqueror (they ensure a lot of loot) it might weird having all those huge cities but huge is relative it's a term in the game it's population over 16000...

The main problem is AI retraining and in order to cope with that you'd probably be better off with a money script that's not so generous to the AI. The balance is really hard to find going from hyperactive to stagnating will make you go . And stagnating is worse than hyperactive IMO.

Human players using steppe factions will probably be in for a crazy ride but I believe playing a Greek or Roman faction on M diff battles and bringing 2 stacks at least for invasion, striking hard and reinforcing with mercs etc will probably be enough to topple even a powerful AS or Ptolies, even if they're retraining if not go raiding take out their recruitment centers in the empire's heart, raze their barracks and the rest of the buildings and they will take a lot of time to regroup.