Boondoc, I picked alternate CQM's for which AC already had data recorded. So I literally picked a few, ran a report on AC to see if any data was already collected, and if I had data for it already I kept that one selected. If another alternate CQM had no data, I abandoned it and selected a different one.
My advice, pick the low hanging fruit. Go for the Alternate CQMs that you already have data on.
However in relation to your other post, when stages 2 and 3 MU come into play we WILL have to meet certain minimum goals. Your points about the ease with which AC identifies our data will become much more relevant.