Sadly, I don't think much is going to change as the consolidation occurs. Pure speculation on my part, as I wish they would expand, but where AA can profitably expand out of BOS is the challenge.
1. The trans-Atlantic and trans-Pacific routes from Boston are already well served by oneWorld partners a la British, Iberia, JAL and Cathay. For Ireland, Aer Lingus has multiple flights. I also doubt that they would push for any other destinations in Europe given the ability to route customers through a oneWorld hub and competition already on the routes (e.g. DL and SkyTeam to AMS, FCO and CDG). Ditto for service to Germany.
2. The other routes which were flown by AA prior to B6 entering the market were the snow-bird flights to Florida, which have been gone for years (with the exception of MIA of course). The flights to Florida do well I would think, judging by the fares we pay and the full loads, but they'd be competing with B6 who has a ton of capacity and Delta who has limited non-stop service. I'm not certain they could make those flights work, even with Embraers.
Frankly, I'm surprised the BUF, SYR, ROC and MDT flights have lasted this long with US. For example, I've seen the Sunday night flight to MDT cancelled many times when waiting for my shuttle flight. I took the MDT flight a hand full of times last year and it was empty. The flights were on what I would assume to be 'peak travel' on Friday and Sunday night.
I'd love to see AA give some options to non-MIA Florida or other points South, but I don't think it's going to happen.