The official explanation for 9/11 is also the simplest possible explanation: terrorists carried out a very low tech and plausible hijacking attack that exploited some rather obvious holes in our airline security.
The 9/11 conspiracy theories are orders of magnitude more complex than this official narrative.
I don't think the JFK "second gunman" theory is more complex than the official truth. In it's simplest form (Oswald worked with another gunman, but there was no overarching conspiracy involving Russia or Martians or lizardmen or whatever pulling the strings) I would argue it's simpler than the official narrative.