On the time thing--Southwest expects you to only "claim" time as PIC if you in fact signed for the jet. So if you're in the right seat, AC qualified, but the guy in the left seat is the AC on the orders, it doesn't matter if you fly hands on the whole flight and he just watches: you weren't "in command" on that flight. This may differ from what the FAA says you can "log" as PIC, but it's a lot better to be able to point to an entry in your time spreadsheet and say, "This is 25 hours where I was sitting right seat with another AC" than having to "prove" that you were the AC when in fact you weren't.
As for which flying job is "better," the demographics of SW hiring show that a higher percentage of military applicants is hired, with lower total hours. This isn't to say that either type of flying (or flyer) is "better" than the other, simply that as a military guy, you'll be part of a smaller "class" of applicants, which has traditionally been hired at a higher rate. As a civvie flyer, you're up against stiffer competition: there are more applicants with civilian backgrounds, with a LOT more hours. Realistically, if you fly for a regional for the next two years, you'll get at most 2000 additional hours, bringing you up to a total of about 3000. I don't think I've met a single civilian flyer at SWA who was hired with less than about 4000-5000 hours (don't quote me, I'm sure there are exceptions, but IMO you need a lot of time to "stand out" as a civilian applicant at SWA). Conversely, in that same two years in the military, you'll get about 1000 hours of PIC time in the Herk, and you'll be pretty much in the ballpark for total time and PIC time with the other military applicants.
Also, if you're unsuccessful at SWA and have to wait to reapply or for the other majors to crank their hiring back up, IMO the military is a better "package" of pay, benefits, and lifestyle than any regional out there, (if you can live with the deployments) and you'll still be building "quality PIC time" every time you fly...
Unless you can find a regional that has the right combination of pay, location, upgrade potential, and lifestyle for you to consider making that a "long term" job in case the opportunity at a major doesn't present itself quickly, I don't think I'd jump from a C-130 left seat into an RJ right seat.