You suspect? Unless they've fixed their time machine, there's definitely nothing AA can do at this point with respect to your getting that upgrade on that flight.

Short-term, I think the best you can hope for from AA is an apology and the knowledge that you're one more person that has brought this issue to their attention. Perhaps separate from AA customer service, you should figure out on your own what the best way to secure upgrades is in the future. I think that this has more or less already been covered here in this thread. The one thing that's missing is the viability of what is perhaps the final option: you get to the gate, there are seats available that weren't available before, but the agent says they can't or won't process the fees. Is it practical to call the EXP desk at that point and have that taken care of, so all the GA has to do is reprint the boarding pass?

Long-term, AA should come up with a way to deal with this better. What CO has done is that at the time you get added to the waitlist for an upgrade, they withdraw the miles and charge your credit card for the co-pay and in the event of London, the extra tax. So, 100% of CO customers in your situation already have all of the ticketing issues resolved before they get to the gate, allowing the GA to fill every available premium seat with an upgrade. If your upgrade doesn't clear, then the upgrade co-pay and extra tax get automatically refunded to your credit card and the miles automatically redeposited without a redeposit or refund service charge.

I know there are training issues and IT issues that make it something that's not very easy for AA to solve. But I would have to think that the lost opportunity in collecting the upgrade co-pays alone would add up to quite a bit on an annual basis, more than enough to pay for the work that needs to be done. And that's ignoring the customer satisfaction issues.