Stability is such a fleeting thing in this economy. Pre 9/11, I would have loved to have worked for ACA. Now I'm glad I'm not (Nothing against you Independence guys and gals. I really hope ya'll make it.)
If growth is any indication of how a company is doing, then I would go with XJT. We hiring a lot and there are all sorts of signs of something big happening here. What that may be is anybody's guess, but something is definitely in the works. Eagle, meanwhile, has cancelled a number of ERJs. Also, we no longer have a flowthrough/flowback agreement with CAL, while Eagle will still receive some AA flowbacks (the actual number may be small, I've heard). On the flip side, our agreement with CAL expires in '07. While I think it will be renewed, there's no guarantee. Then again, there's also talk that AA may want to sell Eagle, so who knows what that could mean.
As far as upgrades, that's like predicting who will win the Superbowl in '09. Right now, I would say that it's going to be alot quicker at XJT, but that can all change tomorrow.
What it boils down to is this: Both companies are as solid as they're going to get in this business. If you have a choice to make, look at domiciles, quality of life, aircraft, etc.
Better yet, just flip a coin.