Maul was definitely a favorite of mine and a pity he was wasted at the end of TPM. But his role was to reveal the Sith and was more muscle than the brain that Palpatine was, so losing him was no big deal to the endgame. Recruiting Dooku to be the charismatic leader of the Separatists while scheming with Palpatine/Sidious on the Republic side was quite interesting. I was disappointed that Dooku had such a small role in the movies (introduced late on Geonosis in AotC and then killed in the Battle of Coruscant very early in the movie). I know the character was developed more in books or Clone Wars, but I just wish he would have lasted a little move into Sith... maybe they could have eliminated Grievous' role all together? Grievous didn't impress me.
Yeah, I think Grievous' function could have been filled just as easily by Dooku. Have Obi chasing him across the galaxy to Utapau, etc. It would actually have made for a more emotional confrontation--he has to find and kill a legendary Jedi Master, Qui-Gon's former teacher, instead of just some random robo-nutcase.
Or keep Dooku where he is but leave Jango Fett alive in II and bring him back in III as the Separatist general and have Obi go after him for a rematch. Or hell, scrap Jango altogether and find a way to get Maul back.
One of the problems with the prequels is the "revolving-door" nature of the villains compared to the OT. The OT had Vader in all three, Palpy in two, and then a variety of disposable baddies (Piett, Ozzel, Needa, Boba). The only one who came close to the Big Two was Tarkin. Thus the final victory in ROTJ is more satisfying than all those "boss battles" (to use a video-game metaphor) in the PT.
Whereas the PT was like supervillains-of-the-week. TPM had Maul--but he was killed. Then AOTC had Dooku and Fett--Fett was killed and Dooku was barely in the movies, as Vlad mentioned. Finally ROTS killed Dooku and introduced Grievous, only to kill him immediately. The Neimoidians/Separatists were in all three, but were really just puppets. Sidious was in all three, but only played an important role in ROTS. And yes, I realize those last two sentences kind of contradict one another. Which probably just proves my point about not knowing where the focus lies. What the PT needed was a tighter focus on a smaller number of baddies.
Let's say we scrapped Jango and Grievous and had Maul fill both those roles. It would have given much greater urgency to Obi's search for him in II and III (both from dramatic/audience standpoint and from Obi's point of view) and Maul's eventual death on Utapau in III--after escaping Obi twice already, on Naboo and Kamino--would be a very satisfying conclusion to a subplot that had been running thru the whole trilogy, six years in real-world time and thirteen in movie time.
Of course, keeping Maul around would necessitate several fundamental changes to the plot structure. Palpy recruits Dooku and then suddenly brings back a borgified Maul and they have to work together while at each others' throats? Palpy converts Qui-Gon and he ends up having to work with Maul, his former enemy? Qui-Gon is the unwitting puppet leader of the Separatists, doesn't know Palpy is a Sith, and Palpy keeps Maul's survival from him?