I'd definitely say their most recent release, the self-titled Dream Theater album. I like it well enough, but I honestly don't understand the praise it has received, and I certainly don't feel it is an album worthy of being self-titled, like it's the best thing they've ever done. I feel there is a sameness found in this album that doesn't have anything that truly differentiates it from other well-defined albums, and I hope the band doesn't remain on this path (I feel their next release will really show where the band is headed). The album has grown on me over time, but overall I can't get into it like I can past releases. I am very much a Portnoy fan, though, and I miss his creative input. I'm not knocking Mangini at all; I think he's fantastic, but I feel I will always be a "classic" DT fan (if classic for DT can be defined as the era of DT that consisted of all 3 original members) over their newer material.
Having said that, I've seen DT live six times, and the last show I saw of theirs, in support of the DT self-titled album, surprised me as the best show I've seen from them.
Lastly, I'm also not very into Train of Thought.
Edit: Looks like people refer to it as DT12. I had no idea.