I have had both cameras - the 1ds2 is still a fine camera up to 800asa and I still use it for a lot of work as the file sizes are that much more convenient for storage, 14 bits made the file sizes jump considerably. The Mk 3 pulls away at 800asa and is very usable at 3200asa - it isnt a huge difference but its there ( and I can lose track of which camera is which looking at high iso files so the difference isn't that big at 100 percent , but the mk three has that extra resolution ), the mk 3 retains colour and dynamic range better at High iso where perversely the mk 2 does better for dynamic range at low iso. I find using capture one software I can make the two cameras almost indistinguishable and detail is very similar - both cameras need to be securely bolted to a tripod with excellent lenses to show any meaningful difference in detail.Sometimes I think the mk 2 is more "ektachrome " and the Mk 3 "kodachrome" as straight from the camera the mk 3 files have that richer , deeper look to them, especially at high iso.
Where the 1ds3 excels is speed and buffer write,handling is easier , but then I never had the problems many mk2 owners seem to have had with handling. I have used it as a sport camera and it worked well despite not being the obvious choice for that type of work. The screen looks nice , but frequently I find it makes files look good when they need work later and I think the Mk 2 screen is a little more honest in that regard. It does help if you are showing the clients files on the camera - you just have to match them later! Jpeg out put is supposed to be better on the Mk 3 but I just think they are both awful, but i have never been able to use jpeg s from the camera anyway.
When compared to medium format the mk 3 is very, very close to a six year old 22mp back I use , but not quite as crisp. I doubt you would see much difference in print. The 22mp back's tones are smoother/deeper too.
The Mk 2 shutter was supposed to be a bit dodgy , but mine has done 70,000 cycles with no problem, my Mk3 shutter started to fail at 25,000 cycles, which is ridiculous for a pro camera at that price. Its probably not typical though .
the self cleaning shutter is good , but I have had to clean it a couple of times with visible dust products to get rid off stubborn bits of dust so I wouldn't rely on it completely.