McGregor always liked the OT and thats one of the reasons he took the role in 1996. You can see how excited he is during pre-production in all the docs--"I'm going to be in a STAR WARS movie!" And then Episode I is actually made and released and his attitude immediately changes to "[eyeroll]". He's always been critical of the PT but tried his best to keep quiet about it because Lucas is such a nice guy and he didn't want to trample a series that already was the most criticised films ever released. But it comes out often because so many people ask him about it. If it was just one film he probably would shrug his shoulders and not think about that one lousy role he took but this was three LONG films that took up three or four years of his life when you combine all the work he did on it. Its true that he's one of the best things about the series but thats a relative comparison when the standard for said films is so low. Its one of McGregor's worst roles in terms of performance because he's such a great actor and usually has pretty strong scripts, but it just so happens that everything else around him in the PT was so lame that he stood out as being "not sucking all the time." I think its just luck for him that he happened to get a role in the PT that wasn't written badly--it wasn't written particularly well, but if you have the right look and attitude and deliver the scripted lines with the sort of personality that the script requires then you will survive.
Contrast that with, say, Hayden Christensen or Natalie Portman--it wouldn't matter who the hell Lucas cast in those roles because theres simply no way to make the script work. Robert Deniro and Maryl Steep would suck just as much. The trick Lucas used was that he made them sign on without a script, before a script or a PT film, on the sole basis of the OT back in 1996--no self respecting actor would accept the role if they actually read the three scripts to the films. Robert Deniro and Maryl Streep, for an example, would never accept the role because they would only have to read the first ten pages and know that there was no way they could do anything but crash and burn. But Christensen and Portman keep quiet about there resentment of the material, for Hayden because it made his career, and for Portman because she basically operates on the principle of not saying anything if you don't have anything good to say. But even still you can find moments when they become more honest and admit that it was basically a dumb series that probably was a waste of time if not for the stardom it gained them. McGregor is the only one that really pulls no punches and tells it like it is.

And really, is it any wonder that he's somewhat resentful of the thing? I mean, the number of character he acted with in AOTC that never existed: Jar Jar, Dexter Jester, Yoda, all of the Kamino guys, the entire Clone War and arena sequence (basically the entire last half of the film), plus all that stuff flying a spaceship and talking to a droid. The only human contact he has in the film is two or three brief scenes with Portman and Christensen (two at the beginning of the film, plus a chase scene and one at the end), one with Christopher Lee (plus a brief stunt sequence at the end, which probably used a double), three with Mace Windu and a digital Yoda, one of which takes place in an all bluescreen stage and was filmed a year after principle photography, and one where he asks a Jedi librarian about a computer. The rest of the film is bluescreen stunts and shots of him walking and looking at stuff. And people wonder why AOTC sucked?

Do you know the only reason why actors complain so little about the film when it sucked so bad? Because it was an easy show and it payed big money. The days were relatively short, almost all of it was shot in a studio--in the case of ROTS, ALL of it was in studio--there was very little pressure or tenseness on set, most people got along and things were technically relatively simple (as far as production). The production company took good care of the cast and crew, paid them very well for it, and Lucas and most of the crew are great people that are pretty laid back and easy to get along with. Its a vacation. Some shows work you 18 hours in wind and rain with a dickhead director screaming at you, a DP that runs his camera crew into the ground, crew getting fired and tempers flaring, tenseness on set all the time, budget cuts and massive scandals, all that bullshit--that stuff happens more than regular people realise on a typical movie, and the prequels had none of that, so thats why most of the cast and crew just take the shitty content in stride and move on to their next project.