Your statement that you thought some of Episode III's plot should have happened in Episode II really forms the core of my argument for why III may possibly be the worst of the three prequels, despite everyone saying it's the best:

It tries to do everything that all three prequels should have done, in the span of one movie.  I and II are almost entirely unnecessary.  Anakin's turn should have happened at the end of II (or we believe Anakin dies at the end of II), and III should have revolved around the repercussions of this, the rise of Darth Vader, and the beginning of his Jedi extermination campaign.

Instead, we got all the events that should have happened during the course of three films that span many years, happening in two hours over the span of, what, a couple weeks?

The third episode sucked too much. I definitely was expecting to watch a GOOD movie when I went to the movie theatre, I didn't expect to see colourful garbage full of unrealistic CGI . The moment when Anakin turns to the dark side is probably the worst and the most illogical moment in the history of movie making.

Padme dyeing because she doesn't want to live ? WTF ? Showing the birth of Luke and Leia and ruining the big surprise of E6 ? Showing that Anakin is Darth Vader and ruining the surprise of E5 ? Showing Yoda, the little philosopher with a lightsaber ? Showing Palpatine with a lightsaber ? The guy who can shoot lightning from his arms ?  Hiring a magnificent actor to play the movie villain and kill him at the beginning of the movie only to introduce a new crappy looking crappy written CGI villain ? A Jedi shooting somebody with a blaster ? Making the powerful OB1 look like a clumsy coward ?

after Clones I was on the fence about how good Sith would be. i was certainly into the trailer (i think all the prequel trailers set you up to expect a good movie).

however - the opening space battle felt soul-less and less dynamic than stuff in the OT (or, say, Starship Troopers) and i was facepalming by the time artoo was igniting fuel with his jets. the yoda/chewie relationship was getting too much etc.

i thought we'd see a lot more around hunting down the jedi, by vader personally rather than the directive 66 montage. the rise - and revenge - of the sith at a more personal level rather than clones doing the dirty work.

the backstory around how yoda arrived at dagobah is disappointing to say the least - was i watching ET for a moment there?!

i didn't think padme would die (though by that point in the movie it seems obvious) because leia has memories of her. there could've been a whole other emotional subplot around a mother giving up her babies and killing herself or whatever, but no.

the more i think about III the more i wonder how anyone can consider it top of the pile.

This is a fairly accurate idea of what I was expecting:

Obi-Wan: A young Jedi named Darth Vader, who was a pupil of mine until he turned to evil, helped the Empire hunt down and destroy the Jedi knights. He betrayed and murdered your father. Now the Jedi are all but extinct. Vader was seduced by the dark side of the Force. 

 Slaughtering younglings, was a "hunt"? I mean that bit of Obi-Wan dialogue sets certain expectations, some of which were changed in Empire and only partially demonstrated in the prequels.

Like Ghostbusters I though Anakin would be a more mature character. Luke's age, but more akin to Han Solo in experience and attitude. Though I would have greatly preferred if his background was simply left in the dark, and that Owen was his real brother from the beginning, I like the idea that he was a slave.

Contrary to many people I expected Anakin's turn to be very evil. Not the Shakespearian drama Lucas so ineptly tried to pull off, not some melodramatic twist, just evil. Anakin should have become Vader knowing into what he would turn into. Lust for power? For knowledge of the Force, becoming the ultimate weapon in the Galaxy (hence his attitude in A New Hope about the Death Star being insignificant compared to the Force). Just in my humble opinion his redemption at the end of Jedi would have been more powerful if it was the redemption of an actually evil and not a tragic man.

In short:

- a better space battle with a story and an impact on the plot of the movie - a set up,  beginning, and an end, like Endor. Instead we got a dozen mindless minutes of ILM's CGI prowess.

- Windu finally getting something better to do. I hoped Lucas would pull a reverse of Jedi throne scenes, just sitting there and manipulating Anakin/Vader to destroy Windu. Mace Windu should have been the best Jedi Knight on par with only Obi-Wan, yet Vader in his prime, with the suit, should have crushed him. I think we desperately needed a show of force from him, why is Darth Vader so feared anyway?!

- Obi-Wans vs Anakin handled differently. Preferably at the beginning of the movie (with Anakin's fall being the final of Ep.II), so he can spent most of the time in the costume. Not like people now presume Vader's costume is like an advanced wheelchair that let's him move at all, but rather the suit should have made him even better at annihilating Jedi.

- I didn't like the concept of the imposing Jedi temple on Coruscant, but if it had to be there, at least we should have seen the stormtroopers assaulting it and defeating the actual Jedi, not some children.

- Proper ending for the entire Separatists story line. Entirely wasted throughout the prequels, even though it had a lot of potential (a twist, what if they had been the good guys?)...

Generally less scenes that strive so hard to be visually game-like cool for teens that they end up being stupid.

A more interesting way for Anakin to have turned to the Dark Side would have been for him to have experienced powerlessness and suffering during the Clone Wars and wanting to end it. He could have also seen ignorance and incompetence causing pain and prolonging the war.

From this, a desire of order and control could have very easily emerged. It would have been easy for Palpatine to then convince him to support his authoritarian ideals, by simply suggesting that the entire conflict was a result of weakness and an excess of liberty ("We can end this destructive conflict and bring order to the galaxy!"). Then he offers the emotionally crushed Anakin the ways of the Dark Side to medicate his personal sense of powerlessness and weakness. It becomes hypnotising and seductive, and he loses his sense of who he was completely ("You don't know the power of the Dark Side! I must obey my master!").

In this way, Anakin's fall could have been initially driven by an understandable desire to end suffering in the galaxy before it was perverted into a lust for control and power. This would mirror nicely with Luke's desire to end the suffering of his firends in Cloud City and the obvious risk this posed for his training.

(This doesn't happen in the prequels. Anakin's mother's death was not a result of the Clone Wars in Episode II or any political conflict, and therefore couldn't reasonably be taken to have effected him a political way - especially since it is even before his mother's death that he expresses sympathy for fascism.)

Erikstormtrooper said:

I expected Anakin to die in the lava. I expected Sidious to bring him back to life using the Dark Side, the catch being that Sidious has to consciously channel the Dark Side for Vader to remain alive. That is Sidious' power over Vader ... the true "Power of the Dark Side" ... the reason Vader "must obey".

Plus, if Anakin really dies, Obi Wan would not have to make the decision to walk away from his dying friend. And he becomes less of a liar in ANH when he tells Luke that Vader murdered his father.

This would have changed the nature of the OT more than anything that was in the Prequels. If Vader is literally an unwilling slave to Empy, then there is no redemption for him as he's being actively coereced to do evil by a very real threat.

And how does it make Obi less of a liar?