These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Palpatine, of course. Add-on materials including the novelization reveal he was angry at Anakin for losing to Obi-Wan and considered leaving him for dead since he was crippled both physically and in his strength with the Force. The only thing that convinced him otherwise was that Anakin would still be powerful even in this state (that said, in the movie he seems only to be impressed that he was alive, and isn't angry at all).
Was done to Mace Windu and Aayla Secura, even though they're both killed onscreen.
Mace's survival is at least somewhat plausible. He loses his hand, gets zapped by lightning, and tossed from a significant height, all of which Jedi are shown to be able to survive throughout the saga (although never all at once.) Secura however, gets shot in the back by at least a dozen troops at near point-blank range, and her body continues to be shot as the camera pans out.
Hilarious in Hindsight: C-3PO remarks as he pilots Padme's ship "that [he] may be getting the hang of this flying." Then Disney's Star Tours ride was revamped and guess who now pilots your Starspeeder 1000?
Hype Backlash: This movie is often lumped together with the other two prequels and carelessly declared to be just as bad.
Idiot Plot: Much of the reason Anakin loses trust in the Jedi and eventually betrays them is due to them not trusting him, thus giving him good reason to do the same. In the end, Anakin's betrayal of the Jedi was as much them pushing him away as him turning his back on them.
But isn't that kinda the point? The Jedi make mistakes, this being one of them. It's not just the fact that Palpatine is manipulating Anakin.
Magnificent Bastard: Palpatine, of course. He plays every single character in the movie like a fiddle and becomes dictator of the entire galaxy by the end of the second act, and by the end of the movie all of his potential enemies are either dead, on the run or on his side. Granted, at least part of this is due to the fact that some of those enemies are not always the brightest folk, but they suspected that something was wrong with him being in power so long and thought at the very least that the Sith might be controlling him, and he still manages to cover his tracks until its too late for them.
Memetic Mutation: Vader's "NOOOOOOOOOOOOOOOO!!!" has since been used as a way (mostly in jest) to show great disapproval over things on forums and message boards.
"You underestimate my power!!!"
"You were the chosen one!", usually in rage comics to show betrayal but full variations of the quotation have been made◊.
"It's over, Anakin. I have the high ground.", since It Makes Sense in Context (just about), but sounds silly anyway.
All of the dialogue between Anakin and Obi-Wan right before and during their duel. Seriously, it's like the writers were trying to make the lines as bad and cheesy as possible.
"From my point of view, the Jedi are evil!" That line alone pretty much sums up the movie. When your Dark Lord of the Sith sounds like the slow member of the debate team, you've got problems.
Eh; some fans saw some flaws. For instance, a lot of scenes- especially earlier ones- seem like the audience is dropping in on the middle of a conversation (suggesting some questionable editing), and even the cast (well, Ewan McGregor at least) were annoyed about the overuse of CGI even compared to the previous films- nearly every single scene involved some amount of green screen in the background, whereas at least parts of the last ones were shot on location, and this can take you out of it a bit.
Yoda may have been feigning his surprise to confuse Sidious. Notice he recovers fairly quickly. On the other hand, Mace Windu was downright stupid: he had a Sith Lord right in front of him, unarmed but still clearly dangerous, and he doesn't even think to incapacitate him or, you know, chop off his hands so he can't use it.
More likely Yoda just underestimated Palpatine. He has casually deflected Force Lightning before (from Dooku in the previous film); he thought he could do so again. Palpatine was stronger than he thought
Anakin for believing absolutely everythingPalpatine tells him, especially his claim to be able of saving Padme after revealing his identity as Darth Sidious (the ultimate source of all the previous attempts on Padme's life).