Could Magic Mountain and Knott's Berry Farm run more roller coaster trains and decrease wait times? Sure, but then there wouldn't be as much incentive for people to buy flash/front-of-the-line passes. I'd be willing to bet the waits are at least partially artificially created to support the flash passes as yet another source of revenue.
Furthermore, the Flash Pass isn't so much a front-of-the-line pass as it is a bypass-most-of-the-line pass. It still deposits you in the loading/unloading area so you could still hypothetically have a 15-20 minute wait depending on how many riders are already in the loading/unloading area.
Edit: Goliath (built in 2000) still routinely has 1-2 hour waits and might even rival Tatsu for most Flash Passed coaster given that X2 was, up until recently, not even able to be added to the standard Flash Pass unless you upgraded to the Gold or Platinum Flash Passes.
Tell me that doesn't smell like an incentive to increase waits to drive sales of Flash Passes in lieu of outright raising prices to control demand.