Although I think the JetBlue agreement is more than meets the eye for the long term, I believe that a "merger" in the typical sense is not the intent.
You may see Eagle finally spun off or sold, er I don't know,, maybe to ,er, let's see, hmmm JETBLUE!
That way Jetblue can become the domestic arm of AA. But to see an outright merger of the two would defeat the purpose of having and sold Eagle with it's lower cost in the first place.
The red herring being the pilots' scope finally being dealt with.