Just so you know, modding the battle mechanics, especially where seiges are concered is extremely difficult. I think of all the many mods here only a few have successfully modded seige battles (one of which was Third Age.) With that said, I agree it would be nice to have the actual keep as a feature of the battle with shooting arrows and what not and walls closer together. Edit: this would also mean that there can be less units stationed in a castle - If you look at for example Eilean Donan castle, that island is nowhere big enough to permanently sustain 2500 men! This would also make siege battles more realistic: 500 people defending and 1000 attacking (which is very doable if you dump your best units in the castle and your ragtag bunch of peasants in a nearby village, especially with the size that they currently use for the map!)
Most of the generals would have been well armoured, even if the rest of the soldiers were not. Its always nice to have a historically accurate mod, so perhaps full plate in the 13th century would be out of place, but it would not be unusual for a general to be fully armoured and his troops a ragtag bunch of peasants