I don't think the plot of Act I is enough to sustain it into an Act II that carried on where Act II stopped. I admit, on first view, I was puzzled by Act II. I admit, it's probably not a one-time experience, and therefore, for that sole reason I think it's flawed.
But I now adore the seemingly unrelated half's that make a satisfying whole. Some of Sondheim's best music, especially the abundantly melodic "Move On". I find "Putting it Together" quite cleverly constructed (and on stage, worked even better in the revival without the original cardboard George concept). Above all, I love the surprise of going from a perfectly constructed Act I, to a more experimental Act II (the start of which, has Act I trapped in the painting).
It's refreshing that Sondheim and Lapine didn't stop with Act I and call it a day. Act II still feels experimental and daring today. Sure, Act I is long enough to be its own play, but the concepts introduced in the first half are expanded on so eloquently in the second.
If anything, the only huge problem I have with Act II is the fact that the modern George is related to Seurat. I find this to be slightly contrived in construct. I feels more forced that it should. Couldn't George be a fan of Seurat's, inspired to create his own unique art from his idol's original? Marie, though she has the beautiful "Children and Art", also feels forced. Though the ending, with Dot and George is quite satisfying (as is the reappearance of our beloved Act I character).
Ultimately, Act II, at least for me, holds up better as time goes on. With more experimental musical theatre (thanks partly to Sunday) happening since the early 80's, the concept feels less alienating than it originally did.
"Broadway...I'll lick you yet!"