Anakin should have been older and it should have been all Kenobi wanting to train him, none of this Qui-Gon (though he's a cool character, he just introduces to many plot holes)
Even with allowing Jedi to love, you could still use have that 3 way struggle i mentioned in my 'add on' to Rebel11_38's prequal idea...just slightly modified to do be a tension/strain forming in their relationship because hes doing the dual Jedi/Sith thing and hidding all this from everyone (well except Palpatine)
I think one of the biggest problems with the PT is as follows:
In A New Hope the movie was made to stand alone if the sequals couldnt be made, so it has a struggle that is fully resolved by the end of the movie. When Empire was made it ended leaving you hanging...it didnt just cut you off but you needed Jedi to find out what happens to the characters.
When Lucas made Phantom Menace he used a similar set up to A New Hope. Yeah, because of our knowledge of the saga as a whole its less so, but it still has that same feel, the only contrary thing to this is Palpatines comment "We'll watch your career with great interest". Attack of the Clones leaves you with a more similar feeling to the one Empire leaves, a what happens now type feeling. Yeah it leaves us with a partial closure, just as Empire did, but theres that definate feeling that there is more to come, your not satisfied with where all the characters currently are. ROTS will (hopefully) wrap it all up. It will obviously have a darker tone because its essentially the start of Emperial rule, but it will end the story line.
What lucas should have done is treat the whole PT as one story (similar to the way it was outlined here, the ideas are a plot outline that covers all three PT movies as a whole). He knew he was gonna make the 2nd and 3rd so why waste valuable story telling time with a conflict that only servers the purpose of bringing all the characters together and then limit yourself to 2 movies that actually tell the story that your trying to tell. This single story should (in my opinion, and i believe others as well) start with Anakin as a teenager (15 ish maybe) the earliest. probably around lukes age (18-20). and like Rebel11_38 said, during the clone war when he and Obi-Wan meet (Obi-Wan senses the force in him/his flying as Qui-Gon did in TPM) and basically follow the story outlined by Rebel11_38 and continue up to the end of the jedi/rise of the empire.
I dont think that we need to see the rule of the empire. I think that the killing off of the Jedi taking place as Palpatine is doing basically what he is doing in the actual prequals is what would be shown in the third movie as stated, and this movie should basically end with the Jedi all but wiped out (Yoda and Obi-Wan are obviously still around, maybe a few other random Jedi, but only nameless Jedi Knights) There would basically be a scene with Palpatine 'taking the throne' and Vader joining him at his side. Something to signify that he's now in control type thing. then maybe a cut with Obi-Wan leaving Luke with the Lars. This could go either way...if the scene is there it give it an ending similar to what i was talking about in Empire...actually to preserve the OT i would def leave out the mention of Leia...and by this arguement i would actually change what i just said so the end is a shot of Obi-Wan taking up residence on Tatooine, then the scene with Palpatine and Vader (I would go from solemn music with obi wan the cue the Imperial march on the last scene) then roll credits.
and as far as my comment about Yoda still being around, i would make it so his fate is unknown...just kind of loose mention of him and dont show him after the last mass slaughtering of the Jedi occurs. what this does is make the movies watchable in PT then OT order without ruining any of the suprises (Vader is lukes father, leia is luke's sister, our first intro to Yoda)
and it would obviously still work watching OT then PT, only prob i could see is people might want some more of those continuity points (a Yoda scene, Luke being left at the lars, leia being left with bail organa)
-Darth Simon
ps sorry for the extremely long post