What you didn't mention in your list of pros and cons was the routing it would require to get to many cities in the northeast or southeast on AA or whether you can get there at all. How would you get to BTV, PWM, PVD, ALB,or MHT on AA, for example? And do you want to backtrack to ORD or DFW or STL to get to a lot of others. On the other hand, Eagle has direct flights to DCA, LGA, BOS and MIA.

Maybe I am not focusing enough on the pros and cons of a FFP, but to me, ease of getting from origin to destination is my #1 criterion.

My suggestion is to look at the list of cities you are most likely to travel to and check out the routing on each carrier before making your final decision.