Both are very nice parks. If you want a good wood coaster, go to Six Flags. Roar is, IMO, the best wood coaster in the state. Plus you have Medusa, which is a pretty good floorless coaster, and Vertical Velocity, their new impulse coaster.
If you are a steel fanatic, you should go to PGA. Vortex isn't bad for a stand up but be prepared for some headbanging. Top Gun is a pretty good invert. Psycho Mouse is a fun family style coaster.
It all depends on what your tastes in coasters are. I only gave you a few ideas of what you can find at each park. If you have some extra time and can make it, Santa Cruz Beach Boardwalk is only 45 minutes to an hour from PGA and has the wonderful Giant Dipper wood coaster, which should not be missed.
X Factor
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SFWoA: An Unofficial Guide
http://sfohio.tripod.com