See, I think the problem you had, especially when refering to the "GLEE trap," was that the musical was basically fluff. You will be hardpressed to find a real, thoughtful musical on broadway, seeing as how the target audience is a bunch of tourists who come into NY to have fun. You wanted something of depth and I don't think any of today's modern shows would give that to you. I'm like that because I'd prefer to see a play rather than a musical, and I am happy I saw Bengel Tiger at the Baghdad Zoo before it closed. I also really really really want to see Jerusalem and/or The Mother Fucker with the Hat. So, all in all, the musical was there to entertain. Many songs were cool, but you are right, some did not really enhance the plot but rather made an emotional point (i.e Colored Girls, Memphis Lives in Me) I do, however, slightly agree with you about the ending. Unlike you, I loved Huey, and after all the shit that happened to him, the last song seemed like a major let down. So, it wasn't so much that I did not like the ending, more so that it left me thinking the play was...unfinished.
But yeah, I can't really think of a lot of musicals where one would say they have "substance." RENT for sure and probably Hair. More music related.