I really, really think there should be a veto mode. it's such an obvious way to make the game more fun for the majority of people playing, and that's what should be the main goal.
How about: you can ban any 3 cards... but only from expansions. Yes some people would be sad they couldn't ban Chapel, but you know, this seems kind of direct. You don't need to worry about buying Cornucopia being bad for you, you can ban Tournament. You can't ban cards from the main set, but you didn't buy that one. If you have no sets you can't ban anything, but we aren't saying "buy something if you want to ban something." The worst case now is buying just a small set and banning 3 cards from it.
This wouldn't be my favorite way of doing it, but it's a way which makes it very hard not to prefer it over how things are now. So, you can buy the smallest expansion and then ban 3 cards. First of all: who would really do this, and secondly, even doing that doesn't really accomplish anything. I don't see anyone getting a significnatly higher rating because he does it, and even if someone got 200 points more because of it, what's the big deal. No ones life was ruined.
You can't ban chapel; well you couldn't ban chapel without a veto mode either. You don't get to play with certain cards; well just make the bans count only for games that you created. If it's important to you to have all cards included, create games yourself. If it's important to you to veto cards, create games yourself. If you don't care, do whatever you want. I just don't understand the decision not to implement somehting like this, in some way or another.