My main gripe, which most DT fans disagree with, is that after Train of Thought, the songs lack soulfulness. What I admired about Dream Theater from the early days through ToT was the band's ability to be virtuoso musicians, but still craft a lot of texture and soul, and breathing room in songs, and make it sound warm. To my ear at least, that started to erode a bit after Jordan joined, and slowly crept out of the music (again, to my ear) with Octavarium. DT hasn't quite been the same to me, since.
I know DT fans will shout examples of soulfulness and warm atmosphere post-TOT. I get it. But it doesn't sound nearly as authentic as it once did. DT to me is more clinical now, more sterile. And I'm not sure what caused it, honestly. Jordan is amazing, and technically, is a master performer. But it'd be unfair of me to blame him. It's just the overall shift the band has had to my ear over the years.
It's an unpopular opinion, and I share it not to rankle the fan base or start any arguments. But the sound just hasn't been there for me over the last several releases.