Well, I think Mike is pretty much spot on about all the Queensryche stuff, although he's way off on the Waters/Floyd comparison, both in reference to Tate/QR, and to himself/DT.
However, I agree with what gmillerdrake and others have said. The 12 Step songs are Dream Theater songs, not Mike Portnoy songs. He wrote the lyrics for them, yes, but the band wrote the music, as a collective. Additionally, my understanding is that it has primarily always been Petrucci and whoever-the-keyboardist-was-at-the-moment who were the actual songwriters, and Mike's main songwriting contributions were lyrics, arrangements and concepts. Mike certainly deserves a lot of credit for making DT what it was, and still is, but to act like he was the mastermind behind the band, even for certain specific songs, is ridiculous.
Furthermore, I always felt that MP's choosing not to play certain songs because they were too close to certain past members was a bit biased. He wouldn't play Space-Dye Vest cause it was written entirely by Kevin Moore.... and yet they still played Wait For Sleep (music & lyrics by Moore) quite regularly throughout their careers, and had no problem playing other songs with Kevin's lyrics (including a certain Top 10 hit single). Likewise, he didn't want to play Anna Lee after Derek left because it was very much a "Derek song", and yet, Mike and JP have both commented that Derek was the driving force behind writing Lines In The Sand, a song that was played many times after Derek left. Why? Because it's MP's favorite song from FII.
Bottom line, if it's on a Dream Theater album, it's a Dream Theater song. And Dream Theater has the right to play any song off a Dream Theater album. Period. Mike chose to leave the band. He has no right to complain about what they can and cannot play.