well, the assassinations of the Jedi (while a cool sequence overall) had some "what, a Jedi was slain by two clone troops? huh" moments. I rationalized it by saying that they were ambushed/taken by surprise, but if you notice many of the ambushed Jedi did realise they were being attacked and thus should have been able to put up more resistance (or Lucas should've had them honestly be ambushed, like shot dead in the back without noticing "something's amiss". Force-precognition does not always work). I was miffed by that scene where the Jedi tried to save Jimmy Smits and got killed WITHOUT surprise by a couple of clone troopers. some friends explained to me that it was a young Jedi, not even a Padewan, really, which is a good explanation. except that Luke was able to do much more as a super-novice and that can't entirely be explained by WELL LUKE IS SUPER POWERED! another scene I'm thinking of is where Mace Windu and two Jedi go to arrest the Emperor (inexplicably not taking Anakin's warning seriously at all and not modifying the party going to meet Palpatine, incidently) and the Emperor kills the two accompanying Jedi in less than two seconds (and they're not surprised). I can accept that the Emperor is totally awesome, but their inability to muster ANY resistance is kind of unbelievable.
one thing this movie really did is crystallize an opinion I had lurking in the back of my mind during Episodes I & II. namely, that the prequels TOTALLY mishandle/ruin Yoda. in the prequels, Yoda is always portrayed in combat as an attitude-heavy chip-on-his-shoulder little bastard. every time he fights, you expect to hear matrix-like dance beats as he curls up his lower lip and makes a face like COME ON, GET SOME! that is soooo not like Yoda in the original films, and I don't think it can be explained away by saying "well yoda had a change of heart after he was beaten by the Emperor!" because they're clearly trying to keep Yoda as the wise, passive-but-powerful type in the non-combat scenes. (I also thought that the end of the Yoda-Emperor combat was mishandled--Lucas did not clearly show that Yoda had been beaten and had to retreat. the whole group I went with was like "ummm did Yoda lose, or fight him to a draw? even if he lost, he BARELY lost!" he really should have gotten pounded at the end and barely escaped in order to give legitimacy to his attitude of "I failed, I'm going into exile".)