I've never used a 1Ds3 (although I do have a 1D3), but as I understand it the IQ is very close up till maybe 3200 ISO, with the 1Ds3 just having the edge in the lower ranges. Once you go beyond 3200 (I'm not sure you can with the 1Ds3) then the 5D2 pulls ahead. Since the IQ of both is so good at low ISOs, unless you push your files hard to extract lots of shadow details in scenes of high dynamic range (where the 5D2 can exhibit banding) I doubt you'd see a meaningful difference in IQ.
As far as focusing goes the centre point on the 5D2 is a solid performer. The peripheral points can be a let down and that can be annoying when you are trying to track and frame a moving subject or just want to shoot quickly without focus/recompose all the time. The 1Ds3 gives you superior AF performance on all AF points and, of course, far more of them, better placed, to make focusing and firing a more reliable and speedy exercise. If all you use is the centre point for AF then there is little to be gained.
On the 1Ds3 you get not only the build and the AF but a faster frame rate, better metering, better meter, better viewfinder, longer lasting battery, greater durability, more customisation options, dual card slots. Of course, Live View is not as well featured and, if the 1Ds3 is the same as the 1D3 in this regard, a rather poor quality preview image which will make it harder to judge focus accuracy as easily as with the 5D2.
As for the price aspect. Personally I think the 1Ds3 is overpriced. It is (was) Canon's flagship camera and they put a price tag on it to fit. Given that you could buy a 1D3 and a 5D2 together (mine cost me £3800 the pair, brand new) for less money than a single 1Ds3 (I've never seen it for less than £4300), in my opinion the pricing logic does not stack up. For many people the price is secondary to the performance/features. If you must have a full frame Canon camera that can handle the worst shooting conditions then there is no option. That's what you pay for. For my money it is long in the tooth and still very expensive, even
second hand.