I (un)fortunately, depending on how you look at it, had a 3 day BBQ road trip with sister in June. Our BBQ tour took us to Houston and the Austin area. During that tour, and between BBQ sampling, we visited both the Cypress and San Marcos outlet malls. As a non-window shopper, all 3 outlets had a dizzying array of stores.
As you and others have already mentioned, both locations have a Premium Outlet, but San Marcos also has the Tanger Outlet. My sister made a point of comparison shopping in many stores and the prices were the same at both locations.
I think what it comes down to is A) Are you going just to window shop? B) Are there certain shops that are a must hit? C) If you are buying "stuff", are you willing to haggle on the price of said stuff? D) And finally, what other activities do you want to do / see?
My sister is a haggling machine and found success at all outlets, but maybe a little more success in San Marcos because there was more competition, which can give you some negotiating power.
To me, I would just go to the Cypress outlet center and find something else to do with your time in the Houston area. If you decide on going to San Marcos, a trip to San Antonio or Austin would be a good idea. Certainly driving through Lockhart, TX to try some great BBQ does not hurt.