That's a part of it as well. It's hard to be the new guy in a band, especially if you are replacing a member whose contributions are so substantial to the distinct sound of the band. I think this is like Sammy Hagar replacing David Lee Roth, Richie Kotzen replacing Paul Gilbert in Mr. Big, Robin Finck, Buckethead and Ron Thal replacing Slash on Guns N Roses (LOL), or Vinnie Vincent and Bruce Kulick replacing Ace Frehley replacing Kiss (Oh my, I mentioned Kiss. LOL). None of them had a happy ending, and we can only hope that MM would share the same fate as JR in becoming an integral part of the band despite coming late into the game.
I would also like to edit my comment about the Pornoy-isms. I made a playlist last night of Metropolis, ACOS, ToT, and Peruvian Skies and I felt that I missed something. I added The Glass Prison and I think my inventory of Portnoy-isms is finally complete.
I also would like to share my view that Awake is the most unique drumming that MP did in that it did not sound like anything he did before, and it is also not something that MP really came back to (which is why no Awake song is in the Portnoy-isms list). I always loved MP's work in Awake, it literally screams "POWER!" and there is a certain rawness to it that is very appealing. Like he did not have to show off how great a drummer he is, so he did not have to do numerous fills but was instead very confident that his drumming sounded great (and it did!).