You have already tried a wrecking ball, might I point out. That was your very first attempt on Sonic’s life, if I recall correctly. It didn’t work so well that time, and when I think upon it, I doubt it would have worked in SRB2’s mechanics, either. Were I you, I would instead try for placing spikes on the ship, to prevent your adversaries from hitting you so conveniently (though they could still hit the window, since you can’t place spikes on that without inhibiting your own ability to see where you’re aiming). However, don’t expect that to be put in SRB2, because it would be a nightmare to code I would imagine.
When it comes to the gate, however, I think the logic behind that was that there had to be a switch to open the gate, because there had to be a way for you to get in.
As for the Eggrock, remember than having only one entrance, at ground-level, would make it a real pain for aircrafts (such as yours) to fly in or out. I would imagine that there would have to be numerous entrances and exits, in fact, so that your robots (or at least your flying robots) could be conveniently and quickly deployed to Earth should any rebellion arise there or somesuch.
And concerning the dining hall, I don’t know about you, but I think having a full-sized dining hall would be rather pointless unless you’re having guests. I’ve never known you to have guests over, not that we exactly know each-other so well. Then again, if you know Wily, then maybe you do invite guests from time to time.