Id go with 2 TC windows each day for every city, separated by at least 8 hours and maintained by the city owner (city owner decides what time is the most appropriate for them). Other than that, I agree with balio, with having militia in the town that can be or doesnt have to nerfed.
If you want to preserve battle militia, I suggest no mercs, no instabuying after capture and reduce maximum limit.
Fix equip requirement for taking the town.
Change the reward to ammo, drugs, weapons, recieving only when some members are in the city.
Also I almost forgot, it wouldnt hurt to have city-wide TC zones.
EDIT:
3. Taking towns the second day after server update is totally imbalanced, as was proved one year ago; so make TC disabled at least during first week.
This is an interesting idea, while I agree it gives huge advantage to the taker, I think it might be part of the game. We all know that Rogues are very good at "recovering" from wipe quickly and thus I assume it as a part of those players´ skills.
Anyway, I wouldnt mind if there was a week period just for the sake of fair play.