I think the booking class that you'd normally be using should play a big role in determining the program.
Will you be using this account enough annually to earn elite status anywhere?
If not then you might just keep using CO since the 50% eqm penalty on cheap fares won't matter. If you'll be flying enough to maintain your AA status plus status in a Skyteam airline then you really need to examine the programs according to what fare classes you use. CO won't be good if you use cheap coach fares, but might be better than Flying Blue if you use Business fares. Flying Blue has a much lower threashold for attaining Elite Plus status as do some of the other non-North American based programs.