I absolutely loved the musical until I read the complete libretto. I still love it because the score is fantastic, but it was then that I saw how flawed it was. Of course, my copy didn't arrive until I'd started fully researching the case, so it was rather unfortunate timing: all of the historical inaccuracies stuck out to me like a very sore thumb.
IMO, the musical could benefit from more subtlety. If they really want to make it an issue of Southern pride and innocence versus northern industrialization and the American answer to the Dreyfus Affair, for heaven's sake, don't make every darn scene include some thinly veiled comment about how Jewish Leo is and how Southern everyone else is. Also, I understand the concept of an anti-hero, but I think that it would be a good idea to make Leo a little more likeable and less of jerk, not to mention less of a stereotype (they made him act like Kyle's cousin in South Park. Leo Frank was born in Texas, for heaven's sake.) I don't think that you have to make Leo a jerk to avoid cliches; I think that the very idea of the case itself defies cliches--normally you would be happy at the very first case in Georgia in which a white man was convicted on a black man's testimony.
I'm also not convinced that they did a good job establishing Conley's guilt. Frank's innocence, yes. Conley's guilt, not so much. And, I don't like how they portrayed Leo and Lucille's relationship, personally, but I understand why they had to do that. I do wish that they would show more of the actual questions disputed in the trial, instead of just focusing on the "was he a pervert?" But I guess time wouldn't allow that.
For that matter, I'd also give poor William Smith a role in it. The man did SO much to try to prove Frank's innocence, it seems really unfair to exclude him.
Jimmy, what are you doing here in the middle of the night? It's almost 9 PM!