I dont think leaving Republic has to be an issue. Life gets in the way sometimes. You spent 5 yrs flying 121? It is a tough career especially when you are not making a whole lot of dough and you can always say you were looking into other opportunites and the economy crushed those plans as soon as you left republic. I think the key here is to show that you want to be a long term employee, that your willing to suck it up and live on reserve or commuting (even if it is not entirely true), and that you are looking for a good company with a stable future to hire you.
ASA/XJT people are definitely starting to leave. I have ran into quite a few who are going to Jetblue, atlas, corporate,... etc and looks like it is just the beginning. There is a little uncertainty with 16 of our aircraft being extended or dropped by United. They have been extremely quiet about these aircraft that are on a short term deal with United and it is due for renewal or extension. The rest of our airplanes are being tied into a new 10 yr CPA with CAL/UAL that is being negotiated right now. Skywest and ASA have plans to re-fleet us with new possibly larger airplanes but nothing is set in stone. Theres a lot of unknows right now but i think the legacies are set to really ramp up hiring in the next 12 months. Getting hired and on the line ASAP building currency and flight time would be a far better place to be for when you get a shot at a major.
Eagle could be forced to compete with other regionals similar to what happened to us in 2006 and their current block hours could be reduced. Every regional has its downside. SJU isnt always a bad thing either. The pay is lower but it is cheaper to live and could be a rewarding experience if your young and single. Good luck.