Wow. You take a day off and the crap hits the fan. As someone who was involved in the Indy debacle, and a current Republic employee I can make the following observations.
First, this is very different from the situation with ACA/Indy. ACA lost its contracts because they stupidly decided to put the Airbus on the same certificate as the CRJs and Dojets, thus violating scope clauses. Bedford has played the certificate shellgame very well, and has things set up so there is no chance a contract can be canceled for scope. Also Independence was flying gas guzzling 50 seat RJs, not larger aircraft like the 170/190. If Independence had CRJ 700s or 900s, the outcome could have been very different. Also Beford will have a good mix of large RJs and narrowbodies, unlike Fly I which did not have narrowbodies for the first 6 months. Independence's operation was running well once they got to 12 319s and 25 RJs. Unfortunately by then Fly I was a dead duck because of the cash burn.
Second, the middle management at Republic is very weak compared to Independence, and cannot sustain a standalone airline. I suspect you will see a lot of Frontier middle management moving over to Indianapolis to teach the people there a lesson in running a real passenger service airline.
Also don't forget about the slots at LGA and DCA Bedford purchased in the US Airways bankruptcy. I think you will see a major shift of flying away from Denver, and towards more profitable routes in the east and southeast. I also expect to see Bedford consolodate the Republic and Frontier certificates. The pilots scope clause requires all the flying be on one list, so there are no incentives to keep the certificates seperate from this perspective. Maintaining multiple certificates is horrendously expensive. There are no restrictions on either certificate so it would not make any sense to keep them seperate. However if Bedford thinks he can get some turboprop flying, Lynx may stay on one certificate, or be combined with Chautauqua. I expect Shuttle to remain as it is, because of the scope clauses at DL and UA.
Bedford made it pretty clear in his latest updates that he does not see much of a future in providing lift to mainline carriers. I guess now we know how he plans to keep the company going in a shrinking market for regional carriers.