I contemplated this for ages a few months ago, 5D vs 1Ds2, then the 5D3 was announced, and then I just bought an EOS 3 yesterday instead.
Last time I looked (which was before the 5D3 was announced, so i'm presuming pricing has changed a bit since), the 5D was tracking around $600-900 depending on condition, and the 1Ds2 was going for $1200-1600 (5D2s at the time were going $1500 and up).
Anyway, I personally think the extra cash is worth it for the 1Ds2, if you can live with the gripped body (I'd need a new bag if I got one though).

Batteries and shutter counts, you'll have to be wary of them no matter which body you buy. Sure, there's a higher chance that a 1Ds2 has been used to death by a pro, but there's also some around that are in collector-condition. Same for a 5D, chances are it's got a lower shutter count because it's more likely to have been a consumer's, but it could be just on the blink of crapping out too.

So if the condition of the bodies you get to choose from are about the same, i'd be picking the 1Ds2 for the much better AF, build, sealing, and those extra few MP...