Booking domestic AA flights is still one of the most efficient uses of Avios. Connections are a fact of life and make the BA scheme less attractive because you pay Avios per sector but you can still pay only 15k instead of a $400-$500 ticket. I've done this a few times in the last month and it has been consistently difficult so I have a bit of advice that might help.

To recap what you should do if looking to book AA flights:

First you begin on aa.com and search using Miles. This will show connecting flights whereas Ba.com is largely useless in this scenario. You must ensure there is Saver availability (booking class T or U for economy/first). What I do then is check the individual flights on Ba.com. Then unfortunately you must call if you want it on one ticket (AA is better than BA with separate tickets if it's all on their metal but I would not like to risk it).

What I have found then happens is that the BA Agent will not be able to "see" at least one of the flights. Today it happened again: the agent confirmed he could see the flights on the website but not on his booking system.

The advice is this: ask the agent to book it anyway by entering the flight numbers and eg T class inventory even though you cannot "see" the flights as available for Avios. I don't know anything about the systems but I'm assuming there is some command line interface. That has worked for me, the system allows it. Apologies if it doesn't work for you but thought it was worth passing it on.