I think one key difference is the substantial change in the writing process, both writing without coming up with drum parts at the same time, and taking longer to find interesting ways for the different instruments to play off each other. With MP, there always seemed to be a drive to keep moving, and to keep a certain pace to the proceedings. That's not a knock against MP; it's a process that has worked very well in a lot of his side projects. For DT though, I think they're much better when they take a bit of time to work things out.
As for the actual drumming; most of the highly skilled stuff Mike Mangini played on the record was very subtle, and could easily be overlooked if one wasn't looking for it. That's one of the things I love about his playing. It's just very musical. He's amazing at playing what suits the music in question, and playing off of the other musicians.