If it were up to me, there are soooo many changes I'd like to see in the prequels. Here are just a few off the top of my head.
First: get rid of R2 and C3PO as they serve no real purpose and just detract from anything going on in the story. Most of their antics on screen were just plain stupid, if not out right annoying and cringe-making. With them in there, it also makes Kenobis' line from SW "I don't seem to remember owning any driods" just sound plain stupid and at best amnesiac (he doesn't remember the cute R2 unit that shared his adventures and saved his life all those years ago???). I really don't think George realises that the series is about Anikin Skywalkers' fall from grace and his redemption through his son (+the whole evil emipre thingy). It really didn't need any other ties or threads to the later episodes at all.
First: I'd replace Hayden 'wot's 'is face' with an elm tree, because it's bound to be less wooden and give a more animated and believable performance in my opinion.
First: get rid of Greg Proops voice in the pod race - grrrr makes me want to kick puppies every time I hear that bit!
First: get rid of the whole podrace. It sucked (no further explanation needed).
First: get rid of the nickname 'Ani', because it makes him sound like a small orfin girl with red hair who sings lots and lots of annoying songs. That nickname is just far too cute. I mean, what self respecting stormtrooper would likely take orders from Darth Vader if they found out his name was Ani? Likely none of them.
First: remove everything that makes you think "holy hell that was stupid!". For example; almost every joke, stupid voice, midi-chlorians, or anything that a 5yo would find incredibly patronising. You know, the stuff that makes you think "just get on with it!" while watching the movie.
First: find a better use for truly great actors like Brian Blessed other than making them sound like retarded Jamaicans. Anyone remember him from The Black Adder1 or Flash Gordon? That guys tallents were sooo wasted in Phantom Menace.
First: get rid of the whole Frankensteins’ monster bit at the end of Revenge of the Sith. That just looked idiotic.
First: use actual models instead of baaaaaad CGI. These 'prequels' not only didn't fit in with the rest of the series superior model effects from the 70/80's, but the CGI just looks far too shiny and has no real 'weight' on the screen. Add to this that if you watch them in episode order, then everything starts out very round in the first 3 movies until Episode 4 when all technology seemed to have jumped backwards about 100 years or more.
First: get rid of the wookies. Sorry, but they were more annoying than Ewoks (hard to believe I know).
First: get rid of the wookie-Tarzan yodel. Comedy mistake#1023: never tell the same joke twice!
First: Keep JarJar and even add a few more scenes with him ... being used in vivisection experiments (anyone see Simon Jansens' death of JarJar asciimation? Classic stuff!).
Phew, I'm almost out of breath now. Man I can't stand those crappy movies. For me the only Star Wars movies are the original ones I saw as a kid in the 70's and 80's. I try real hard to forget that those other abominations even exist.
Many apologies if I went over board, but those movies make me get passionate about something which was a HUGE part of my life as a kid.
... anyways, that's just my 2c.