I think some degree of customizing walls would be good, every city didnt have identical walls to each other like in RTW, "epic walls" for example all looked identical. You should be able to design them to an extent, not that dissimilar from formations in battle.

There should be levels of fortification, archers should exactly have to be placed in the towers for towers to fire etc I think sieges really need improvement if MTW2 is going to be a success.