For one: higher level castle gates should be reinforced. It is way to easy to open high level castle gates with a ballista... In MTW 1, i think, ballistas and catapults were not effective against much beyond a wooden fort. I think, that's the way it should be. As to trebuchets: one had to pick their location very carefully in order for them not to be decimated by castle defenses. I guess, the solution is to increase the castle defense range.