I wasn't that impressed by either of the new songs from Keys, but they at least felt like Yes, just not top-shelf Yes. It's hard to describe; all the pieces were there, but they didn't fit right, or something. From Keys II, only "Mind Drive" really excites me. To me, it works just as well as any other epic of theirs. I like each of the main themes, and I like the flow between them. The rest are interesting ideas which for some reason they decided to just repeat over and over, driving them down from pretty good to mediocre. Even the instrumental (whose name escapes me) starts as a good idea, but there's just not enough there, and repeating it eight times doesn't change that.
To answer your question, though, the difference is that The Ladder just didn't gel for me. There are some good songs, but the bad ones really bring it down. (There are songs I always skip, and with Keys I can at least listen straight through.) And admittedly, I was probably too aware that Wakeman had left again and whatever keys I was hearing were being played by some guy named Igor who had no Yes cred, so maybe I was biased. But I did give it a chance. They promised a return to form, and the samples they released on the net got me pretty excited. I bought it right away, and listened to it in the car a few times before passing judgement, but man, some of it was just bad.
Maybe I should give The Ladder another shot. I was disappointed by Keys, and felt a lot better about Keys II, although it hasn't aged well. The Ladder never really worked for me, so I never listen to it anymore, but I do remember hearing some good stuff.