JR, MA changes from camera to camera... A few years ago I shot with 2 50Ds and I borrowed a 24-70 from Canon's CPS for a few weeks... one camera i needed an MA of like -2 and the other 50D i needed a MA of almost +10... Also were you shooting in full auto AF or were you shooting in spot AF or expanded AF? I've gotten feedback from a few users that full auto AF may be "off" a bit but when i told them to shoot spot or expanded, all of a sudden their images got increasingly sharper. Lastly the 2 RAW softwares, one a beta which may do wonders for you, or may irk you and the other DPP which has a bug... All those factors could factored into your results... all but one, full auto AF, not being the cameras fault, per se, but the software for DPP being a canon issue. Also unlike adobe, canon doesn't allow people with preproduction cameras to shoot raw let alone use beta versions of DPP, so they could get no feedback that it's buggy... Perhaps if they stopped that policy but allowed them access to beta versions and keep that under the NDA agreement, they could head off some of these issues in the future.
Neuro i fully agree with you about expectations... Sad thing is from a XXD or 7D user, the 5d3 will likely be more than they could have asked for, but for 1d and prior 5d users, i can see how it could have been seen as a disappointment. I personally see it both ways, but since i never really faulted the 5d2s image quality when I had my 5d2, I just hated the body/af/etc the new features and any improvement of IQ and ISO is welcome. Is it on paper as impressive of DR and IQ as the D800, probably not, but i'm not going to waste time fretting about it either.