There's no doubt that Rudess could play circles around Pinnella, but I don't care about that. It's the same thing live - Rudess has his tilting keyboards and fancy tablets and wizard hats, but who cares? Outside of a few piano passages, the guy is a robot. He plays with almost zero feeling, worrying more about "thickening up the sound" on albums (which he doesn't need to do because the band also has Petrucci and Myung) than crafting memorable solos and passages. There's never a point when I'm listening to any song where I think "You know what? This song really needs nine separate keyboard parts right about now." The guy just overplays on everything he touches, and it gets exhausting.
Pinnella, on the other hand, is still a virtuoso without overdoing anything. The way he plays piano and synth lines in polymeter over whatever sweet riff that Romeo and Lepond are playing is very unique to me. I'm not going to sit here and say that many of his solos are memorable... hell, I don't think many of Romeo's solos are memorable! But Symphony X is a band that works best when each instrument brings technical playing into a bigger picture, and Pinnella is a huge part of that sound (particularly on the stronger, pre-Paradise Lost albums). Dream Theater writes great songs at times, but I've always found them more predictable in that the instrumental sections always sound like it's someone else's turn to wank.
Pinnella for me, and it's not even close.