I had a very hard time choosing between both airlines, both are in the top tier as far as regionals go. In the end it came down to which place was going to give me the best QOL, at the time it was Eagle, I wanted an ORD base and it looked like SKW would have been a Fresno base.
Things have changed now, and both companies will allow for an ORD base off the bat.
With the bases being equal would I still have chosen Eagle knowing what I know now? Yes I would have, only 15 days of reserve, holding all weekends off, never been junior manned, never been extended(other while on reserve). I have 85 people below me in ORD, time to CA has dropped 1.5 years in the last three months, all of the flowbacks are on their way out, management has started a major airline career placement program. The feeling now is that in addition to the flowbacks going back to AA, all of the Eagle CAs with number will flow in the next few years(which is most of our CA's) and us new hires will all get AA numbers when we make CA(as long as we dont choose Eagle rights).
I dont know much of SKW, other then I have a few friends who work there and they love it also, say it is a great place, quick time to CA, and great equipment. The only thing that would possibly scare me off would be the lack of a union on the property to protect the good contract that they have in place over there.
In the end if you wind up at either place you will be very glad that you are there.