Was Boba Fett really the 'bad guy' in Empire? He had two or three scenes. This goes back to the overblown importance placed on Fett by some fans and, as a result (and I think far more unfortunately), Lucas. Jango Fett was a terrible 'bad guy'. There were about zero reasons to include him or Boba Fett's backstory in the prequels, and certainly little reason to make it a major plot point for an entire film.

Back to Darth Maul, I think what the films lacked was a consistency in the villian department. Three separate villians who 'look cool' (maybe not so much Count Dooku) all of whom get no character development, no sustained tension surrounding any of them, etc. I realize that ultimately the revelation of Palpatine as Sith Lord is something akin to Vader's presence in the original films, but there was something very real about Vader... Maul had a lot of potential, but it wasn't written in there at all. He was introduced, had a single line of dialogue, fought two lightsaber battles, and died. Thats IT. That is terribly weak character writing! Why not leave him this mysterious figure (with perhaps a bit more screentime to build that tension) and have more revealed into the second movie? Why not have him last all three movies, as a near-equal to Anakin who is finally destroyed by him? I mean, there are a million ways that story could've been told better. All I do is sigh anymore when I think about any of these movies and how wasted their potential was.