I commute regularly BOS-ORD. Both UA/CO and AA have regular flights, so it really doesn't matter too much from a schedule standpoint.

I personally prefer AA, but if you are going to be in the 25k-50k eqm range, you may be happier on United. You will get Economy Plus access for more legroom, where on AA you would be limited to the 12 exit row seats available on each flight. On either airline you are unlikely to be upgraded as a Gold/Premier flyer, but you would probably have higher chances on AA.