Jesus Christ, when they cut off your nuts were they kind enough to use an anaesthetic? Or do they use it as a model experience for when you listen to Jack Johnson's "Bubble Toes" and cry about how sweet it is with your fiance?
Tool was born on the same wave of rock as Nirvana and Soundgarden. It's not Mallcore, nor would I classify it as overwhelmingly dark. Tool has been best described as progressive art-rock. The singer doesn't scream his way through his music, nor does his voice dominate the sound the song.
If you consider them pseudo-intellectual, I can only assume that you're finding music that is "intellectual" somewhere else (I would love to know if there are more "intellectual" bands), because Tool is about as good as it gets.
Perhaps it's just that Tool presents the argument for questioning society so much more eloquently than other bands. For example, the song "Lateralus" catalogues Maynard's philosophical development from traditional modes of right and wrong to more relativistic and open thinking. One of my favorite tracks because I'm intimately familiar with the transition.
The seven to eight minute songs give the sound time to develop. I know you're used to radio-friendly singles, but there is merit to having a bit more time to develop a musical landscape. It's nice having artists that allow a song time to breathe.
@Sandy: "All Systems Red" is a beautiful song. I love the opening.
Truth is a possession.