The show was, in my opinion, not nearly as great as everyone says.
I never thought there was a lot of disagreement that the show had its flaws, especially in the second act. And of course, a lot of people saw different versions as Wolfe tried to tweak it.
But as you note, the show features some great performances. And one of the things I admired about it is that it really was trying something new, albeit with old songs and a familiar backstage musical storyline, about a chapter of Broadway history I knew nothing about. When deciding on shows to see, I was more interested in seeing Shuffle Along than in another jukebox musical or yet another familiar film with songs added. It's sadly ironic that this show looks to be facing the same fate as the original musical. It will be forgotten, yet another Shuffle Along "revival" (alas, it wasn't one) that didn't work, with not even a cast recording. In this case, it seems to have been done in by a combination of bad luck and poor planning.