While I do think that a lot of musicals were clearly best musical material, and I personally think they have been stronger than other best musical winners, I haven't seen some of the shows that these works lost to, so I can't compare it (I wish Into the Woods had won best musical, but I haven't seen Phantom so I can't compare. And even though I think Music Man is kind of weak, I can't honestly say West Side Story deserved the tony since I haven't seen it(I know, but I don't watch bootlegs unless I'm obsessed with a show or am doing it, and I haven't had any oppurtunities to see WSS).
However, I can tell with upmost certainity that in 2002, Urinetown deserved the tony award over Thoroughly Modern Millie. Urinetown is, in my opinion, is one of the better shows with a spoof of musicals, as a)It is only mentioned by two characters, meaning that they are the only ones who can break the fourth wall, so the narrative flows much more smoothly, b)it was the first of its kind and it wasn't trying to ride upon a trend and instead was trying to tell a story, c)it had a strong plot behind it that could've stood on its own without the lampshading aspects of the musical, and d) It happens to blend an exceptionally depressing storyline with highbrow humor that is extremely hilarious, which is a hard thing to do well.
Millie, while being a decent show that deserved its nomination, is subpar to Urinetown. Even when I saw a performance of Millie done by incredibly talented actors and actresses, I look back upon this and realize it to be kind of boring. You really need sparks like Sutton Foster to perform roles such as these, and while it was a good musical, I felt that it was nothing groundbreaking like Urinetown.
Also, kind of off-topic , but the tony awards need to get straight what counts as a featured actor/actress. Marian in Music Man? John Jasper (AKA the leading male) in The Mystery of Edwin Drood? Featured actresses and actors are characters that, while serving importance to the plot as a whole, are more involved in the subplots of the musical. Marian is the love interest of the main character, has 3 large solo songs, 1 duet, is sung to in Madam the Librarian, serves major importance to the plot, and develops the character of Harold Hill. John Jasper is featured heavily in seven songs, and has solos in 2 songs. Get your act together, Tony Awards.