Given that B6 has costs about 2/3's of AA's, there will be no merger between AA and B6 because of incompatible cost structures.
What is possible is that AA could be trying to woo JetBlue to oneworld but, based on DOJ precedent, AA and B6 can never coordinate schedules or fares or share domestic revenues.
What could happen is that B6 could BUY AA and then could reduce AA's costs to B6 levels in order to compete in the domestic market.... I'll grant you that is far fetched but if AA is unable to turn the company around, they will do what they need to do in order to salvage some value from the company.
There is nothing that stops AE from continuing to operate should AMR file for BK; if anything it is more likely that AA would take AE into BK, strip out costs, and then sell it before exiting. But that also could happen with other key parts of AA's network as well - as I noted above.
What is NOT going to happen is that AA will merge with anyone with its current cost structure - which means AA's current labor contracts or labor relations.