I always felt that he was trying mirror ANH with TPM....
Qui Gon = Ben Kenobi - both die at the end
Obi-Wan = Han Solo - the more "mature" hero
Anakin = Luke - the wide-eyed younger hero
Amidala = Leia - the heroic female
Jar Jar = Chewbacca - the non-human in the party bound by a life debt to a member of the party
If Anakin had been Luke's age and Jar Jar had been the quiet exiled warrior who had been banished for leading forces on the loosing side of a Gungan civil war, the overall plot of TPM would have worked MUCH better IMHO.
Move the events of TPM closer to AOTC and have the Sith Apprentice be Count Dooku from the beginning - as much as folks like Darth Maul, he was ultimately a distraction.
With this change up you get the added bonus of initially the Jedi thinking that Dooku is the Sith Master when he reveals to Qui Gon and Obi-Wan that he's a Sith and that deflects from any suspicions that might have existed regarding Palpatine and it's not until Dooku is killed that he reveals himself to be the Sith Lord pulling the strings all along.
So at the end of EP1, just have Dooku defeat his former apprentice (the reverse of what happens in ANH where the apprentice defeats his former master) and Obi-Wan force Dooku to flee. With Anakin being older and an accomplished pilot (as already established by Obi-Wan in EP6), it makes putting him a Naboo fighter make all that much more sense and the fact that his latent force powers helps him win the day (again just like Luke did with the Death Star) and that is what ultimately convinces Obi-Wan to start training him.
All of the rest of the plots could have flowed from that point on. Dooku could have still moved on to forming the Confederacy. Palpatine/Sidious could have still played both sides. The Clone Army could have been something that they started working on in the past as a part of their grand plan. Palpatine could/would have still been elected Supreme Chancellor out of sympathy for the fact that his system was invaded.
I'm not saying that that re-write is the be-all/end-all awesome plot, but it at least helps get rid of the over-the-top kiddie elements that even my 8 year old son at the time thought were ridiculous.