The only catch, for me, is what to do with the scene early in ROTS, when Anakin killed Tyranus at Palpatine's behest. Honestly, I felt that that scene was handled very awkwardly, and didn't show Anakin's vulnerability to the dark side as much as it did his vulnerability to suggestion from Palpatine. Maybe it could be excised completely, or something.
See the way I envisioned it was something like you have Maul show off is uber ninja lightsaber skills in TPM. Then he matches Force wits with Yoda in Clones giving the impression he's one serious BAMF.
Then in the opening sequence he once again bests Anakin, but of course R2 saves the day and Maul retreats to the other seps on Mustafar. The movies progresses (mostly) as is, Palps christens Vader and sends him off to kill Maul as an initiation thing. So, ultimately we're left with this scenario:
Anakin Skywalker cannot defeat Maul, only Darth Fucking Vader can.