No major disadvantages (to my knowledge). I always use AA.com to purchase IB/BA tickets because it's almost always cheaper for some reason. Not sure if AA gets any money out of it, though I hope it helps to steer a little extra business their way.
It's possible that you may not be able to use IB's check-in kiosks. I'm not sure on that point. Actually, I don't even know if AA.com can issue e-tickets on IB. I purchased a trip in early 2004 that was on paper tickets. I had a trip in mid-2005 that was on BA metal with IB code (same price, higher minimum miles per segment) that was issued as an e-ticket. If this is an issue for you, may want to check with AA first.