That's a good 3 cents worth Chess.
I know that YPAO/MCACC is not perfect as I've seen some of the problems that you've alluded to. Most of the problems I've seen/heard of had nothing to do with the EQ portion of the setup but rather with the "phase(wiring)" check and "speaker size" check. I think many ppl are confused about the auto setup in that they think the EQ portion of the setup and the wiring, distance, size and level checks are all one-in-the-same.
Granted, if the ,d,s,l checks are not correct then the EQ will not be right, but the ,d,s,l setups can all be easily done manually though the onscreen menus and then skipped during the auto setup (at least on the Yamaha RX-V 1400/2400). For example, my 2400 often "sees" one of my speakers as being wired out of phase and "sees" my surrounds as large (possibly because they are rated down to 65Hz) which has nothing to do with the EQ setup. So I go into "manual setup" and give it the correct values. However, the 2400 is accurate on the distance and level checks.
