The opinion that Tool is the main course and APC just a side dish is so wrong, on so many levels.
First and foremost, APC isn't about Maynard, or never was supposed to be. APC is not Maynard's "side project", or Maynard's band at all. APC is Billy Howerdel's band, of which Maynard Keenan was a member.
Anyway, Maynard Keenan hijacked the band and now it's just an empty pit for ideas that he doesn't want to use with Tool or his terrible solo project, Puscifer.
Billy probably should have gone with a different singer if he didn't want to get sidelined in his own band, but Maynard being in APC got the band way more attention than they would have otherwise.
It seems like bringing Maynard into a band is like bringing MP into a band; once you do, it's never really "yours" again. Just by being there, Maynard naturally exerts a certain amount of creative control, and draws a faction of zealous fanboys who only like the project because of him.