First and easiest of all, get rid of JarJar. Replace him with someone else less annoying who can actually speak intelligible english or just eliminate the part entirely, i don't care.
Second and a lot more complicated, tone down Anakin.
Make him about four years older. A lot of the stuff that seemed over the top in a kid would be more realistic in a pre-teen. It would also make Yoda's statement about him being too old more reasonable. (I guess they need to get them at two or three to make sure they can successfully brainwash out all emotions?)
Get rid of the virgin birth and the prophecy. How do they help the plot? Isn't being incredibly strong in the force impressive enough by itself?
Get rid of the !@$%! midiclorians. Do they serve any purpose other than to provide a numerical analysis as to exactly how cool Anakin is and to prop up the stupid virgin-birth thing?
Somewhat related to the tone down Anakin thing, it would be nice if the battle with the Droid Control ship was a little more realistic. I mean, who designs a ship with the main reactor core sitting in the middle of the hanger/flight deck? You're just asking for trouble the first time someone makes a bad landing.
Overall Episode 2 had a _lot_ less wrong with it. Other than a few quibbles about numbers there's not much to fix that doesn't relate to the problems with the first movie.
I alread expressed my general annoyance with the whole prophecy thing, now for some specifics. How exactly do they expect the prophecized one to restore balance to the force? What exactly is wrong with it? The only imbalance particularly obvious to the viewer is that there are several hundred good jedi and only one or two bad jedi.  Obviously the quickest way to address that imbalance would be to slaughter all the good jedi, which i'm sure isn't what they really had in mind.
There was one throw-away line along the lines of "is it time to reveal that we're not as strong in the force as we once were?" I'm going to guess that _maybe_ this has something to do with the imbalance in the force, but that wasn't actually stated. If that's the case then it would have made a whole lot more sense if it was revealed sometime around when the prophecy first was.
So how exactly are they weak in the force? Has the amount they can psychically lift or the speed at which they can move it been cut in half? Are they only able to see half as much of the future? Are they unable to notice a Sith lord while he's sitting across the table and laughing in their faces? (Oh wait, they don't know about that yet) Are the current jedi getting weaker or is it just each new generation of jedi weaker than the previous one?
Furthermore how exactly does Anakin bring balance to the force? The only thing i can think of is the already mentioned slaughtering of the imbalanced numbers of jedi. I suppose i shouldn't complain about this one too much since they have time to do something in episode 3, but it really doesn't seem like anything obvious has changed by the time we get to episode 4.
 I really wonder what kind of power source they use in the ships and battle stations. If you shoot at a a gas engine you might get an explosion if you rupture the fuel tank. If you shoot at normal (for us) battery you're going to get acid leaking all over but no explosion. If you shoot at a nuclear reactor you're either going to get a meltdown or a more low key leakage of radiation but no explosion. So i wonder what everyone is using for reactors that has a failure mode of blowing up. And skipping ahead a bit, if shooting a reactor causes a gigantic explosion why is it that slicing through a lightsaber, which must contain a huge amount of energy, just causes a few sparks? If i ever design a battle station instead of having a reactor i'm just going to stock it with racks and racks of lightsaber power packs.
 In the begining scroll-text thing it says that several thousand systems are thinking about rebelling. Later on Doku says that if they succeed in their plan then ten thousand systems would probably join their cause. The second statement _could_ be hyperbole, but since the first statement is given in a factual context i think the second statement is also true, or at least realistic.
Given that it seems that there must be at least about 15k systems in the republic (several + 10.) Further i would posit that that number is less than 50% of the systems. The Republic is still clearly run in a, well, democratic-republic context. Despite the implied corruption and beaurocracy if the majority of the senante decides on something they're able to do whatever they want. Since it seems to be one senator per planet if greater than 50% of the planets could agree on something as drastic as succession they could probably also agree on several less extreme courses of action that they could force through the senate. So i believe the number of systems in the Republic must be at _least_ 30k and quite likely significantly more. 100k would be a roundabout guess.
So where are all the jedi? Coruscant is portrayed as the center of jedi learning and leadership so it should have the highest density of jedi in the galaxy. They hear about the army on wherever it is and rush off to the rescue. The implication that every able-bodied adult jedi is going to help, which turns out to be all of about 100. It's certainly possible that lots of jedi were out on missions at the time, and it's certainly possible that lots of jedi have permenant stations on particular Republic planets and so couldn't participate within the given time-frame, but it still doesn't make any sense. How many jedi per planet are there supposed to be? I know they're rare but how rare exactly, one in a million? One in a billion? There should be at least _one_ jedi per average sized planet, and i would expect quite a few more. That would mean at _least_ 30k jedi in existance. Some reference was made that the jedi were a police force, not an army. One jedi per planet isn't even that.
 Okay, yoda says that there are always two sith lords. Earlier it is said that they thought all the sith lords had been wiped out. This does not make sense.
At one point the jedi knew of the existance of the sith lords, and at some point after that they thought all the sith lords had been wiped out. It is implied in the movie, and stated outright elsewhere i believe, that the jedi were in conflict with them and participated in the (believed) destruction. At some other point the jedi came by the idea that there are always two sith lords, master and apprentice.
Now the basic question, which shall be elaborated on, if there are _two_ how do you manage to _think_ they've all been wiped out but be wrong? You kill one and then lose count?
Now it is possible that there were more than two at some point in the past when the jedi were in conflict with them. This would make a lot of sense to me, since all the jedi's in the galaxy vs two sith lords is not much of a fight, and like i said it's hard to lose track while counting to two. However this possibility brings up the question of how they decided there were always two in the first pkace.
The jedi can't have decided that there are always two of them _after_ they thought they were wiped out because that obviosuly would violate the theory that they didn't exist any more, so with this chain of logic they must have decided they always came in twos while there were in fact a lot more than two of them.
However that pretty much proves that there's _not_ always two of them. There might be four, or six, or eight, etc. And of course since they get killed from time to time there might be just one. What's the mean time on replacement of the apprentice? And clearly if there can be lots of them there must be some way to migrate from there being two of them to there being four of them. Presumably if the apprentice becomes fully trained without getting killed and one of the two doesn't manage to kill the other, they must eventually go their seperate ways and each start a new pair.
So really either the jedi are just _dumb_, or there are not always two of them. There may certainly be a strong tendency for sith to work in pairs but it's not a certainty. So if you find one sith lord you'll _probably_ find at _least_ one more, but possibly a lot more than that.
 It's hard to tell how much of what Anakin says about the kinds of relationships jedi are allowed to have is the truth, and how much is a self-serving re-interpretation. It seems that either the jedi go with the "girl on every planet" type philosophy and just leave lots of children scattered about which presumably get picked up later if they develop an afinity to the force, or they're not allowed to have any relationships at all and are slowly breeding themselves out of existance. This might explain why the jedi are losing their powers, it's not an imbalance of the force, it's a refusal to accept basic genetics :)
Oh, and finally, _please_ cut down on the reuse of places and names. Yoda and Obi-wan being in the movies makes sense. Tatoine, R2-D2, C-3PO, Lars and Beru, Jabba and Chewbacca do _not_. I was ammused by someone's comment that "Tatoine is the first place they'll look, so we'll just hide him there after they look," but it's still inexcusably stupid.
I vaguely wonder why they decided on Naboo rather than Alderan. Hiding Leia on the planet her mother was from would be pretty stupid but that didn't stop them with Tatoine. We didn't actually get to see any of it in the original trilogy so it would have been interesting to get more background on Leia. Of course maybe he didn't want us getting too depressed about the fact it was all going to get blown up anyways. Or perhaps he didn't want people to start cheering when Alderan gets blown up in Episode 4 and yelling "Take that JarJar!"