First of all, the whole industry is in the crapper. AA and AE are no exception. Relatively speaking, AMR is in better position than most of the other major carriers. Southwest is squeaking out a profit, but in tough times, the low-cost carriers usually do. Like it or not, this is a very cyclical industry with very high capital costs. When your customer base goes away (business travellers) your costs still don't change but your revenues do.
As far as "issues" at AMR . . . . well:
1. the AA pilots' contract came up for renewal last August and those talks are ongoing without much progress as is usual. The longer the companies can slow-roll the contract, the longer they have lower costs.
2. AA has not asked for employee concessions.
3. Force Majuere provisions have been cancelled.
4. AMR is being forced to comply with AE ASM restrictions that they themselves agreed to in the last contract. These ASM restrictions were triggered by having AA pilots on furlough and ratio of AE and AA flying. They don't like it and want unilateral relief from the AA pilots.
5. In a cynical attempt to skirt the ASM cap, AMR is transferring 14 RJs to outsourcing company TSA for them to operate under a "reverse" code-share in STL. This is also a clear violation of the AE ALPA scope contract. In the last contract, AE pilots gave up considerable compensation in return for a combining of a hodge-podge of front companies operating as AE into a single entity and a scope clause that forbid exactly the kind of thing that AMR and TSA is trying to scam. This will, in all certainty, NOT hold up in court.
6. The AA pilots' union (APA) has proposed the absorption of AE into AA to operate as a single company and single seniority list. AMR has flatly rejected this proposal. Not surprising since they have something like 10 more years on a sweetheart contract. AE pilots generally have reacted favorably to the APA general proposal.
Bottom line is that the same fight over scope is going on all over the industry. All the major airlines would like to break their unions, and they see NOW as the time to get the wedges in. At the very least, the major airlines' managements are seriously trying to change their compensation structure to be like their commuter afflilates. Transferring flying to outsourcing companies with cheap labor gives them flexibility and freedom from those pesky labor contracts that force them to deal fairly with their employees.
Many corporate executives in the industry would like to see the entire industry "internationalized" with ownership and cabotage restrictions lifted. This could result in very cheap labor brought in from South America, Europe, Eastern Europe, and elsewhere to replace higher paid American airline workers (pilots and flight attendants especially).