Almost 3 years ago I was in your same position. I was looking at Flex because of the pay, but chose EJA cause of their size. I was lucky. I work for EJA and love it here. I can confirm that on average of once a month I get a former RTA guy asking about how to get on at EJA.
One big point of contention for these guys (besides the insurance) is the lumping together of the sick time and vacation time. I was told (not saying this is accurate, maybe a flt ops guy can help out) that flt ops gets 12 days off a year to use anyway they want, sick days, personal days, vacation. A weak point in this system is that if you do get something serious, or break a leg and are out for 6 weeks (like a friend of mine who got menegitis) you have used your vacation up for a couple years and would have a period of 2-3 years with 0 days off. Am I understanding this right? For the record EJAs vacation is 2 weeks off for the first 5 years then 3, then 4 after 10 years. We accrue 1 sick day a month buildable to around 60 days or so, then you start losing the unused ones (as if somebody would be that foolish).
I agree with the above post that says go with the one that hires you first. They are both decent companies that both have a plenty of room for things to get better. At this level this is the equivilent of choosing between Delta and AA with no offers from either. Good Luck.