The biggest difference to me, when I hear MM play, is I can tell that he's playing as a member of the group. See, what I was beginning to hear with Portnoy's playing was a sort of "I'm the band leader, so everyone should follow what I do" type of playing. It seemed to me that the other members were following the drums. Like, JP would play something that would fit with MPs beat. Towards the end of MPs tenure, it started to sound as though the drums were driving the band, and all the others were just following his lead.
What I hear with MM is much more subtle, but suitable for the music. It's exactly what JR said in the documentary, I can hear MM listening and understanding exactly what every other member of the band is playing, and he plays a groove that compliments the others.
If you want specifics: At the end of the instrumental break in Outcry, where JR is playing a subtle piano part, MM plays very softly on symbols. That particular part--not necessarily couldn't be played--but wouldn't, by MP, for whatever reason. I find that part to be the most amazing act of selflessness on the whole album. It's as if Mangini's saying, "Ok Jordan, it's your time to shine. I'll just hang back and enjoy."