Some good ones have been mentioned, like the busses. They're better than nothing, and for us, better than driving, but still, I don't think they are what Walt had in mind...
Untrained CMs is another one. Not their fault usually, its just that the training isn't what it used to be.
The gift shops after rides only bother me if they are an out of place obstruction. If its themed and the aisles are reasonable, I don't mind. (Unfortunately most have aisles that are too narrow, making it difficult to escape, er, get through.)
To me, the problems with saving seats at parades and such is a direct result of the limited scheduling. Lining up for Spectro wouldn't be nearly the ordeal if it were held more often.
Of course there's the rude guests and unruly kids, but really, I think they makeup a very small minority. Its just that the hundreds of well-behaved fun loving people around us don't usually catch our attention. I'll gladly put up with the out of control kid here and there (even in a "nice" restaurant) if it means there are a whole bunch of others around enjoying the "magic".
All in all, though, even the things that I don't agree with don't bother me while we are there.