This has probably been stated, but ADToE and DT12 aren't different because of Mangini IMO. That's a naive statement, as Portnoy didn't have TOO much to do with the writing process outside of drums and 12 step suite. Regardless, it's noticeable that DT was on their way to the sound of DT12 and ADToE. And I'm not saying that in a bad way, but Black Clouds does sound like a transition to the sound of ADToE and DT12.
Personally, I think that ADToE and DT12 are weaker, and more generic sounding. The songs aren't as diverse sounding; but they have a habit of having an interesting intro that leads to the same generic sound (Behind the Veil, Bridges in the Sky) or just a part that really seperates it from the rest of the song/album (IT middle strings part, most of Enigma Machine). I don't think it's the end of good DT, though. Just change of sound.