Train of Thought is very high on my list of Dream Theater albums. Definitely in the top 5. I love the angry and aggressive mood it sets and Petrucci's guitar playing is incredible. My only slight complaint about it is the relative lack of distinctive keyboard sounds.
Also JR is mixed a bit lower overall, which contributes to that I think. On As I Am, you could forget they even have a keyboardist until it gets to the bridge section, when the big strings come in.
But there are some cool keyboard sounds on there too, still a bit more inventive to my ears than sounds on recent albums. I especially love the big sliding portamento on the strings sound in SoC, where it slides from that rumbly low root note to the higher notes, creating that crazy synthetic string sound. One of my favourite things about the song.
That's one reason I really enjoy the Budokan versions of the ToT songs, because the keys are mixed much more present, from the xylophone type sound in the pre-chorus of As I Am, to the evil pads behind the spoken verse of This Dying Soul, which just elevate that section well above the studio version.
I also think it's great how well he manages to incorporate quite a bit of his piano work into such heavy songs. It works really well.
I do agree it's a bit cut back on the keys though, especially coming off of SFAM/SDOIT, which are JR's most keyboard driven albums with DT.