It would be great to hear Dream Theater do something really percussive, or else really ambient. I'd love for them to use elements of noise like Steven Wilson did on Insurgentes, or else more electronic influences. In short, I agree with the OP. DT are amazing musicians who write very good progressive rock, but rarely have they really pushed the boundaries of rock music. Instead, they've displayed extreme competence within the boundaries of progressive rock and metal. Musically, though, they are far less daring than the prog rock greats, i.e: Yes, King Crimson, Genesis, Pink Floyd. Same goes for Transatlantic. Dream Theater and Transatlantic may be the most skilled musicians in the genre, but there are contemporary bands and artists who are far more daring when it comes to pushing the boundaries and being "progressive" in the dictionary sense (Radiohead, Steven Wilson, Sigur Ros, Bjork, to name just a few).
Whether "more daring" = better? That's subjective, of course