1. EB mod had a great idea for discouraging prolonged city sieges. Fe. two or three turns in, your general would obtain a trait - a morale penalty. And it would only get worse from that point onward. As for RSII, f.e. when you lay a siege to a remote maritime city, you should also have to ensure the participation of your fleet, as a means of balancing your army's supply needs, and also blocking enemy supply. If you don't, you should have an army which is not willing to fight. Can something like this be done?
2. I really don't like the fact that AI is able to recruit fresh army with +4 experience. I know it is intended to produce a more challenging gameplay, but it just isn't realistic at all, and devaluates the whole experience concept. On the other hand, it is pretty realistic to be able to recruit an army with much higher morale at your homeland towns, than in conquered ones.
3. Slave Trader idea has a great potential. Can it somehow be linked to a process of changing structure of a town's populace, which should at the end result in conversion of Cultural and Economic building. Maybe it can be triggered when a town revolts, or offered as a choice at some point.
4. Maybe some sort of partial recruitment during sieges should be enabled, at least for the non-elite skirmishers... It doesn't make sense that you have a besieged settlement with 10.000 men inside, non of which is able to carry a weapon.