I think killing Maul right away was the was the single biggest mistake (and there were plenty) the PT did.
The three movies were severely lacking some kind of cohesion. If they had a single primary villain out front, with Palps mostly in the background, I think the narrative would have been better for it.
More importantly however, had the film ended with Maul slaying Qui-Gon, facerolling Obi-Wan, and finishing with a bad-ass walk-off, I think the film would have been accepted (perceptually) more positively. The ending would have become the focus and, even with everything else being equal, the other "annoying" aspects of the film would have been overlooked to some degree.
I also think the "unknown" factor would only have helped here because instead of the interwebz lashing out against Jar-Jar for three years, it would be aflutter with discussion on who the fuck was this guy who just showed up out of nowhere and smacked the heroes around.
And the whole idea of butthurt Obi spending the ten year interim chasing down this "phantom" would have made for a much more interesting starting point for Clones.
And I really don't know why Lucas felt the need to get rid of him. Tyranus was pointless, and Grevious was just silly. It was like he was worried people wouldn't have accepted the ten year aging, but then gave us an ancient Lee anyway.
I wonder if he had noticed Maul's overwhelming popularity sooner, if he would have made some last minute changes.
I completely agree with you. Maul could have very easily taken the roles that both Tyranus and Grievous filled in AOTC and ROTS. I think it would have been cool if we discovered that the leader of the Separatist movement in AOTC turned out to be the same Sith that killed Qui-Gon and nearly killed Obi-Wan in TPM; certainly more impactful than the leader being some guy we'd never heard of before.
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.