I do understand about the first problem. I had the exact same thing happened to me about a year ago. I put in for mileage upgrade, it cleared, I show up at TPA, and the TA is asking for a cert #??? Anyway a 10 minute call took care of it, but to this day I still don't understand why I had to make that call??? Why couldn't the TA make the call? Anyway, it was upsetting and frustrating. My cellphone was cutting out, it was loud, blah, blah, blah, but at the end I ended up sitting in J on a 9+ hour flight for about $400 plus the miles. Should it have worked better? SURE, it could have, but let's be realistic, it wasn't that big of a deal. I got over it and I'm sure you will too.
The second problem? The airlines have a fare scheme. You and I could argue, debate the good and bad of the scheme till the day we die, but nobody will listen anyway. The more important part is this. The $2000 that AA gave away? it's not really $2000. It may be $500 at best. They gave away vouchers for future AA flights. A $500 voucher entitles the holder to a flight that's sold for that amount. Do you think that it actually costs AA $500 to transport you to the destination of your choice? Of course it does not.
I agree with the above replies. They do have problems, but what you describe is not a major problem, it's a hiccup that happens to ALL airlines. I saw an episode of "Airline" where Southwest was overbooked by something like 40 or so. I can't even imagine that.