Back to the OP, you can't really compare Tool to Dream Theater...the musical styles of both are completely different, even if they both fall under the somewhat generic term "heavy metal" or "hard rock."
Dream Theater is a progressive rock band...influenced by classic bands like Rush, Genesis, Queen, etc. If you listen to the compilation cover track on Change of Seasons, you definitely get a better feel for their musical influences...also, most of the members of Dream Theater are classically trained...I believe a few of them studies at the Berkeley school in Boston...not many of their songs work for the video or radio play format, as they are simply too long.
Tool I think more adequately fits into the angst filled music of the early to mid 1990s...I think there are more similarities between Tool and NIN, then Tool and DT. Tool's lyrics definitely have some depth to them...certainly make a statement...but most of their songs are video/radio friendly, perhaps explaining why they are more well known.
I like both bands for different reasons...I also like the side projects from the respective members of each band.
But Tool & DT...it's an apples and oranges comparison.