My personal opinion:
Whichever regional gives you the soonest class date with the least committment. Second to that, whichever regional hasn't been hiring for as long as possible. Since regional (or really, all airline) hiring happens in waves, you would much rather be on the front end of that wave so you have plenty of hiring under you, which means less time on reserve and more time either aggressively time building or bidding min credit and having paid time off at home. I would take being a senior lineholder at GoJet over being a 12-month reserve at Endeavor any day of the week. Failing that, here's my personal list:
Endeavor
Envoy
Skywest
PSA
Horizon
Mesa
Piedmont
CommuteAir
Republic
GoJet
Air Wisconsin
Endeavor, Envoy, Skywest, Republic, and PSA are all about as safe as it gets for regionals. I just couldn't bring myself to rank Republic very highly because of that contract. I consider Endeavor to be the best because I think that Delta is the most financially sound legacy right now, Endeavor has a good airplane with an Embraer 175 program on the way, and their basing has something for everyone east of the Mississippi (and if you're moving in base, DTW, MSP, and ATL are all pretty affordable). Skywest loses a few points in my book because of their metering, which would slow your progression to a legacy (given that Hawaiian probably won't exist in the next year or two, Skywest will be working for EVERY legacy). Horizon has a good airframe, but they haven't hired much at all in recent years and with the upcoming Hawaiian merger, there's a lot of uncertainty as to what their role would be in the combined airline. Mesa always seems on the verge of folding but at this point, so much money has been pumped into them that it's clear that United won't let them fail, at least not until the next whipsaw. CommuteAir and Piedmont are a good amount lower down because their future is much more in question being 145 operators (and no, CommuteAir social media team, having a single Embraer 170 that hasn't flown in 6+ months doesn't count). What distinguishes GoJet and Air Wisconsin from CommuteAir and Mesa is poor management and training. GoJet, despite having a relatively decent 550, is owned by HK who is aging and his kids don't have an interest in keeping the business going. While CommuteAir and Mesa are well known for having training programs that will practically drag you across the finish line against your will, GoJet and Air Wisconsin are known to be pretty difficult with a high wash-out rate. And for Air Wisconsin, after all the heartache of getting through their training...you get the honor of flying a CRJ-200 with a broken APU.
All of that said, the primary goal of a regional for the vast majority of pilots should be this: get in and get out. I wouldn't sacrifice a single month of seniority at my career airline just to have had it better at, say, Endeavor than, say, CommuteAir. Go to the first regional that won't ruin your life (finanically/PRIA-wise, it's a given that any of them will ruin you emotionally), take your type ride, and then update your apps every month or less until you get a call from an airline that is in more control of its own destiny