With respect to the OP I don't think there is a problem with sieges being too short. Under the current engine you have to spend at least a turn sieging a settlement which has any sort of wall, even if it is a 500-people village(if you spend the first turn building the siege equipment and then assault straight away). With RTW turn being about 6 months this is plenty long enough for a siege of almost any city, and since the MTW2 turn will be about 2 years there will not be a problem there.
As for the bombardment of the walls taking weeks and months, the only way to simulate this would be to have the walls already breached when you start the assault, but I don't think too many people would like that. Or perhaps you could start the assault with the walls badly damaged but still holding, and you would then deliver the final blow which brings them down. But then, you would have to attack a predetermined section of the wall?
By the way, o'etaipos makes an excellent point about the size of the sieging army. It is not realistic to be able to siege Constantinople with a three-unit army, even if the garrison is small.