What would I keep? That's a hard one to answer. There are elements/characters from the PT I felt had potential, or the potential for potential (XD) - that they could have been very good if they had been heavily thought/fleshed out, but are very, very weak as they are.

I'd keep Padmé, Qui-Gon, Maul, Dooku, and Grevious, but I'd heavily retool them, so much so that they'd only superficially resemble the originals.

As for what I'd keep intact (or relatively intact):

The dogmatic/legalistic nature of the Jedi. The idea that the Jedi, a less than perfect arrogance-fueled organization, practically set one of their own up for the fall is one with much potential, and sets the whole fall of Anakin, the destruction of the old Jedi Order, the rise of Luke, and the creation of the new Jedi Order in a whole new, interesting, and inspiring light.

Watto. I can't help but like him. I'd just make him more sinister - to make him more suitable as an antagonist.

The "deathsticks" scene. I love the exchange between Obi-Wan and Elan Sleazebaggano (that is a stupid name, isn't it) and Obi-Wan's nonchalant tone of voice and demeanour. I know a lot of OOT fans hate this scene, but other than the "Sleazebaggano" name, I just don't see what the problem with it is.

I like Dex. I don't like the CGI he's made of, but I like his personality. I'd definately stick him in somewhere.

And ... that's all I've got for now.