You could make very cool movies with Darth Maul as a villain, but not the SW prequels. The whole idea for Sith apprentices was to keep the place warm for Darth Vader. You couldn't have characters like Darth Maul around for very long, he would have outshined Vader. Even the Emperor Lucas kept in the shadows until episode 3, when Anakin became Vader. Lucas had to walk the line between providing cool "minor villains" and not undermining Vader's image as the OT's main villain. If anything, Maul was "too cool".

This worked well enough for Lucas' purposes. Kids loved Anakin (and still do, the prequels are still very popular with kids who were too young to see them in theaters, just like happened with the OT), and sympathized with his situation. Obi-Wan was there merely to provide a standard of Jedi apprentice to compare with Anakin later. Lucas had earlier ideas where Obi-Wan was Qui-Gon and Anakin a teenager (mostly because he didn't want to work with a kid actor. Lucas is from the school of direction that let the actors do the acting and you can't direct kids like that), but he realized this didn't work and he needed Anakin to be younger in the first movie.

The whole problem is that the fans expected the prequels to be a set of movies providing a viewing experience very similar to the OT, and with a very similar tone. Most of the fan "fixes" are focussed on that angle. Way back in 1984, Lucas was saying if he ever made the prequels they would be very different movies because that's what the story required. They would be darker, with a more complex plot involving economy and politics rather than a war, with characters very different from the OT's rebel heroes as they were not warriors but politicians, and that he would require something goofier than Chewbacca and Threepio thrown in the mix as comic relief to be able to tell that story in a way that would appeal to young kids. Much the same way he decided to switch from Wookies to Ewoks in the OT (he decided along the way Wookie were not primitive enough, and that trying to get the fun/kid friendly tone he wanted in this episode would make the Wookies look silly. Let's keep in mind the SW episode Lucas has the most reservations on and has said a few times was "off" the tone he wanted to keep for the series is ESB.. even the famous Vader-Luke cliffhanger wasn't planned. It came later because of Lucas' worries that if he confirmed Vader was Luke's father at the end of ESB after he cut his hand, it would be too much for 7 y.o. to handle. He asked experts and they told him the scenes were OK for kids as long as he let them a door open for denial, if they could believe Vader lied to Lukeand he kept the confirmation (Luke's scene in the falcon) too subtle for kids. And that's how it became a cliffhanger - though Lucas was surprised a lot of the adult audience also went into denial!).

That's exactly how he dealt with the prequels in the end. They're still movies aimed primarly at 7-10 y.o. set on a background complex storyline that he developped by small touches only. The politico-economical storyline is there and remains coherent (especially when you fill the storytelling gaps yourself), but its development isn't the center of the prequels. Too complex for kids, most of the deleted scenes were political pieces like Senate scenes, meetings and exposition that explained further the political plot - and in the end Lucas decided he didn't need those and they would bore kids. The centerpiece was Anakin, and it was primordial for Lucas that this aspect of the story was told on a level attractive and understandable for kids. Even Padmé's and Anakin's "love story", so ridiculed, isn't so bad when you consider it's a love story told at the level of 7-10 y.o. boys who didn't need, or wouldn't have liked, anything more than that. Simplistic and not credible yes.. for adults, not for young kids.

75% of the criticism levelled at the SW prequels is irrelevant when you judge them in the proper context as kid movies.

Yes, the OT captivated a wider audience, but Lucas never meant to compromise on his goals to make movies for 7-10 y.o, just because older people also liked them. The major difference between the reception of the OT vs. the PT is that back then adults who liked SW didn't mind these were kid movies. Those who mind it for the PT are by and large found in the audience that grew up on the OT, refuse to see they were kid movies as they still enjoy them as adults and for some reason expected Lucas to make the PT with them in mind, instead of reaching to today's 7-10 y.o.