I thought about this a lil bit and I think I came up w/ some decent suggestions.
First, make sure that the one semester wait period at the second school applies to transfer students. Some schools only make first years wait.
Second, take every opportunity possible to visit the fraternities at the second school and have your friends introduce you not only to their brothers but members of the first org you're considering and any others on campus! You could get there and find out that fraternity #3 is perfect for you.
Now make three lists. On the first list put all the reasons that YOU want to go Greek. Nobody else will see the list so be completely honest! On the second list put all the reasons you want to be AAA (fraternity #1). On the third list put all the reasons you want to be BBB.
Now take each list and mark each reason as either short term (during college) or long term (after college). Ex: The college is boring as heck and you want the extra social life...short term. You want all the networking contacts...long term.
If your reasons for going Greek are mostly short term, go with the house that gives you the most short term benefits. And vice versa.
Hopefully this helps some and I didn't just confuse you. Let us know what you decide!