Skyway
As Propsync said, I'd look elsewhere, unless you really just want to fly out of MKE for a while and move on ASAP.
With an AirTran takeover, it's anybody's guess what happens. Maybe Skyway gets bigger jets, maybe Skyway's Operating Certificate gets sold off and Skywest does all the flying, maybe AirTran drops the RJ thing entirely, your guess is as good as mine. Even if Midwest stays on its' own, most of us had very serious doubts about Skyway's future, courtesy of Midwest's use of Skywest on Skyway and Midwest routes. There's no way to convince a pilot group that everything is going to be ok when your airline is shrinking and dying while at the same time your holding company has contracted out for another airline to start flying in your colors on your old routes. But really, I'd apply to an airline that has a brighter future (hell, try Skywest and you too can fly out of MKE!).
I also quit working for Skyway (in June) after working there for 7 years. Your career opportunities are extremely limited there, and the only reason for working there is some quick 121 time and probably a Beech 1900 type. But things are so bad morale and quality-of-life-wise, that I'd really lean towards another regional, one that at least had an academic chance of providing you with a job long term if need be.
In the airline industry, you must go off of what you see and know, not rumors and what-ifs. You need to take a snapshot of any airline you want to work for and consider that, not get all wrapped up in planes they MIGHT buy or plans they MAY follow up on. So take a look at what's happening at Skyway, how many planes they have, staffing, schedules, etc, and how they're treated by their owners, Midwest Airlines.
The problem is, the people you would work with are really great there, and I even got along well with management. The training guys were top notch, and maintenance was awesome. Even flying the Dorkjet was a blast. Just career-wise, it was a dead end, at least for me.
Whatever you choose, good luck!
ps- I knew as soon as I saw the Strongbad avatar who you were, propsync! Did you ever find anyone to play golf with?