I kinda have to go musician-by-musician for this one.
Russell Allen v. James LaBrie I know a lot of people disagree here, but I like both voices about as much as each other, even though they're totally different. Allen is easily one of the most versatile, talented vocalists I've ever heard, and he does it without losing the emotive aspect of singing. LaBrie I like for different reasons--his voice is very unusual, and in a lot of ways easier for me to sing along with. (Although too much of that snarling from Awake hurts my throat! For an example of that, see the Bands/Projects thread.

) However, having never heard either band live I can't say anything about how they each do in concert.
Michael Romeo v. John Petrucci: Tough call. On one hand, Romeo is clearly the faster, cleverer player...on the other, I have not heard as much acoustic work out of him as I have from Petrucci, and I wish I did. Ultimately I think Romeo is better just slightly, but Petrucci has his high points, too.
John Myung v. Thomas Miller v. Michael LePond: Too bad you don't hear much of Myung in later DT albums, because he's let rip with some riffs in places that reminded me a lot of Thomas Miller, who's easily one of the best bassists I've ever heard...absolutely inhuman! Between those two, I can't tell who the winner would be...I'd have to hear the two duke it out onstage to know which is better. LePond...well, he just doesn't seem to be as prominent in the mix as Miller would be, although he is very skilled indeed. Myung may just have the edge over him.
Michael Pinnella v. Kevin Moore v. Jordan Rudess: If I knew anything about Sherinian I'd add him here, but I don't. I would say that in technical terms, Pinnella demonstrates his much more than Kevin Moore. However, Moore does seem to know how to USE what skills he has to greatest effect, overall I like him as much as Pinnella. But Jordan Rudess...sorry, but Pinnella DOMINATES Rudess. Rudess is all chops and no composition or feeling AND I think he's at least in great part responsible for tarnishing DT's former glory. Pinnella, on the other hand, is highly skilled, but the arrangements he helps create have a sweeping, emotional quality. I'd like to see Rudess make a whole orchestra come to life!!!
Jason Rullo v. Mike Portnoy: Easy--Rullo wins this hands-down. Better sense of rhythm, more interesting riffs (or whatever you call them when it's percussion you're talking about), and better mixing of the drumset into the overall sound. (Now, Walling had the same annoying kind of mix Portnoy uses...however, his skill makes up for it by STILL solidly beating Portnoy to a pulp.)
Overall, I think that Portnoy and Rudess are the weak points that keep me from enjoying all of DT's output as opposed to just some of it. Symphony X is the better band, but Dream Theater does have some talent that shouldn't be ignored. Symphony X blows the current stuff out of the water--but the Kevin Moore-influenced DT is tougher competition by a lot.