At Building Panoramics we have both the mk1 and 2 5D's, and we have found, as Mikael Risedal says, the AF module seems identical.
When Canon produces a cheaper version of the 5D MK3 it's inevitable that some of the features left out cause different people different issues. For me I would have much rather had no GPS or Wi Fi, instead having a metal top cover. On our 5Ds the pentaprisms have had some knocks, especially the 7 year old mk1. However the top of the 6D does seem robust enough. Also I would have preferred the joystick for AF control, but then again we use manual focus most of the time, and the 6D at least accepts manual focusing screens. I don't like translucent LCD screens that Nikon and now Canon is using in the MK3 and 7D. I find it harder to focus manually. ( I suspect the 6D takes these mk2 screens as much of this part of the camera is straight from the mk2).
"Crippling" the MK2 by using the MK1 AF didn't stop many pros from shunning the 1Ds MK3 in favour of the smaller cheaper 5Dmk2. To give Canon all credit they accepted this, listened to their customer base who demanded a more professional MK2 - and they delivered - the MK3.
The problem is that here in the UK all gear is much more expensive than in the US for example. As Infared says you can get a 5D mk3 body for $2600. In the UK these are down to about £2350. If you take the $/£ exchange rate your US price would be £1640 in the UK !
Basically our friends in the US can get a 5D mk3 for the price we have to pay for the 6D