Here is a point I do not believe anyone has touched upon yet, except for briefly by Adami:
For the next Dream Theater album, the vocals need to be better. I am not talking about style, technique, or even choruses; more specifically, I am talking about verses.
The only vocal parts I ever seem to remember from Dream Theater songs are choruses. I never noticed it until this past year, when artists like John Mayer and R.E.M. came to dominate my playlist, whose respective catalogs are filled to the brim with songs where the verses are the highlight. Dream Theater verses, for the most part, seem like they are there only 'cause they have to be.
Oh, I don't know. I agree that the choruses are more memorable, but then "Without warning" is possibly one of the coolest verses I've heard in anything. Ever. I do think that Dream Theater put a hell of a lot of emphasis on the choruses, but I don't really think they neglect the verses. I think the choruses are just that much stronger because they want them to punch you in the gut.
Part of it might be that their verses are quite unique from a technical perspective - they try and do all these wayward things and throw in arpeggios and odd riffs. The chorus is where they kind of allow themselves to take a breather and just throw in some really catchy power chords. So I'm almost tempted to say it's because they've left room for the vocals in the chorus. I mean, take AROP. It's got that weird middle-eastern riff going all the way through. That riff's the catchiest riff I've heard in ages. I could sing that riff for hours. The chorus is the only place in the song where they really go "right, ease up chaps, it's time for a spot of LaBrie!" It's the only bit in a song where they leave space for the vocals to carry it.
I think that's just an occupational hazard of being a progressive rock band. They're composers who like to try and fill every second with some top notch music. I mean, if you listen to Muse's instrumentals (as in, songs with the vocals removed), they're very basic. Repetitive almost, but that's cool because the vocals are almost the keystone, and they use a rockin' bass riff as the backdrop rather than a main feature. Throw on a Dream Theater instrumental, on the other hand, and it's chock full of nifty bits all the way through - it chops and changes more than a chameleon slicing up some carrots. They leave some room for the vocals and don't properly go all out frets-on-fire till the instrumental section, but with Dream Theater the emphasis has always been on the musicianship and writing excellent music. If there's something to sing along to, all the better.
I don't think the verses are weak, though, vocally. But there are elements of truth to what you say, and I think they quite wisely stand back and don't saturate the verses with all these interweaving melodies.