Hmmm... I can.  A paragraph synposis of the prequel trilogy as is doesn't really read any better than anything I've seen here.  There are some why's that naturally won't be answered in a simple summary.  That doesn't mean the idea is weak, only unfinished.  If you had a movie by Speedball and you could point out something that wasn't explained then, Triadkd, your complaints, which are really just questions, would have merit.
Anyways, obviously the biggies: different director, less CGI, less cutesey ness.  More of the good stuff (and there WAS some, wasn't there?) and LESS of the weak stuff.  I'd actuall suggest making the movies longer and LOTR-epic.  My main thought is that all the pieces were there, and that a slight bit of tweaking could have made the prequels truly awesome.
First movie: Phantom Menace
Well, the FIRST and MOST important thing in TPM is: older Anakin.  Make him 11, 12, or 13, the age of accountability.  This is a child who has a capablity of showing a dark side, or showing hints of being already tainted, making the complaints about him being 'too old' and 'having much fear in him' have HUGE merit.  A cute 8 year old who is scared of losing his mother is but two years older than a youngling, and hardly 'fear ridden' when compared with his peers.   It also gives his facination with Padme a bit more oomph.  And best of all, it gives him flying a ship and blowing up the enemy, fueled by his dark destructive tendencies and assisted by R2-D2 a great deal of credibility.  Less of the Bad. 
Darth Maul.  Add in a couple more fight scenes for him, giving him a chance to really show off the Sith's ruthlessness by slaughtering a city or something (and thus making resonance with Anakin's slaughter later).  I'd also add a character building moment ( a conversation with Qui-Gonn during the tatooine duel) where his philosphy of death can be shown off, thus foreshadowing powerful both Qui-Gon's and his own deaths.  I think having him defeated by Obi-wan on raw power was unwise, and I think a more 'outsmarted' approach (followed by a killing swipe) would be more interesting.  I also think hinting at the existance of Teras Kasi, where an unarmed Maul battles against Obi wan with Saber would have been interesting.  But, if it were me, I actually would have had a Maul with robotic legs show up in number 3 to cause havoc.  MORE OF THE GOOD.
Jar Jar binks.  What can be done to fix this? The comic relief is, unfortunately necessary, especially in a family film like this.  I say let Ahmed Best have more say in his lines.  Let him be more unintentionally funny than goofy slapstic.  Oh, yeah... one, MAYBE two slapstick moments, not endless tounge electrocuting and "yousas."  And let Obi-Wan's dislike of him be clear, giving the audience a vent for this, essentially, cartoon character stuck into a live action movie.  LESS OF THE BAD.
Trade Federation.  Good on the basis, one thing I ask: Let their home base not bear ANY resemblance to the death star... no big circles in the middle... let's at least PRETEND to be origional.  I think the biggest and best arguement for the giving up on battle droids in favor of clone troopers would be to have the Jedi turn the battle droids on the trade federation by taking the main control panel.  Thus, the droids could have been much better, MORE OF THE GOOD.
Podracing/Tatooine/Midiclorians: I say leave it in, and giving Anakin the handicap of being 'too big' this year after his growth spurt.  And while I think the idea of him being immaculately concieved by the Force is utterly rediculous, I think I would have been happy with Shmi being found by Watto pregnant with no memory of where she came from.  Everyone can believe what they want.  LESS OF THE BAD.
Yep I think that takes care of that.  I could speak on the other two movies, but honestly, that setup takes care of just about everything. (oh well, I'm long anyway)
Clone Wars
Foreshadow the clones in TPM and get to them quicker.  Yoda should not be flipping like a green ball of fur.  Let him strike with power and direct speed, but still be agile and hard to hit as a mother... I like his horizontal spins, but the vetical ones upset me.  Yoda running through a crowd of stormtroopers relieving them of their feet would be so cool to me.  Less Bad.
The overall issue would be to make Anakin and Padme's love affair interesting and less forced.  They would have to travel (not from one field to another) and Anakin would actually protect her life from a viable threat, again, more of his darkside comes out.  I would actually have them marry and in crisis to the point where Anakin is about to turn all on his own by the end of two, when the wars start.  Someone's idea about Dooku being a mixed side jedi working the sith from the inside against the Jedi's protests is awesome to me.   That would have been so hot.  
Another small issue is the arena scene and battle.  I think having a more varied terrain for Jedi battles: more on-the-steps action, battling in tunnels, jumping from platform to platform, tandem moves and such, would have given a much better picture of the scale of battle that was supposed to be occuring.  
Revenge of the Sith
Anakins fall, was, imho the biggest shortcoming of the prequels.  I never bought it.  The jump from 1 to 2 was drastic an unforeshadowed as it was, but when Anakin went all out against everyone, I just didn't see the need for it... I didn't see Anakin as being that emotionally unstable.  A more shakespearean approach: Anakin believing Padme to be dead, would have been FAR more believable a push to the darkside, and given credibility to everything he did after that: True desperation while giving the audience a real sense of the tragedy that is Darth Vader.
I also would have put him in Vader gear MINUS the helmet and chest plate with buttons (as though they were life support and the costume itself was symbolic) dramatically just before he stormed the Jedi temple, perhaps even still carrying Dooku's lightsaber for dual bladed fury... I would even get artful and have him only attack with the red and only defend with the blue. Heh.
Regardless, I feel all the pieces are there, but that some tweaking would have put the Prequel Trilogy on that LOTR level.