One thing I agree with a lot of people here on is that Anakin should've been more evil and definitely dark side in AOTC. His sudden switch in ROTS was only made better by ADM's fanedit. In fact, the original story had a much better switch point (where Palpatine reveals himself to Anakin), but George said he changed it because it was to soon. No, actually, it was the perfect spot. But anyway.
I think I expected a lot of things to be cleared up. Things like "There's something familiar about this place", "I must obey him", "And he was a good friend". After AOTC came out, a friend of mine said "WTH? They were never friends so what's up with the line in ANH?" This is plain to anyone that watches them in the order of release. Even in the comics, Obi-Wan was constantly on Anakin's case. That, to me, is not much of a friend. I was also hoping for a better explanation of why 3PO didn't remember Tattooine even though as ROTS got closer it became more apparent that a memory wipe was in store for him.
What I never expected was that as the PT moved along, the Star Wars galaxy would become smaller and smaller, to the point where Yoda and Chewbacca are now friends. Was that really necessary? How about instead of blowing the screen time and that one little scene, we show Yoda go to Dagobah and maybe explain why he went to Dagobah. Nah, can't do that.
Oh well, now I just pretend they don't exist.