If price was no object then of course the D3 is better, except that the integrated grip is a double edged sword...
When I have the grip mounted I would rather have a D3. But I also often shoot without the grip because a grip creates issues of transport, weight, bulk, etc. And because Nikon has never put a dedicated AF lock button on their grips my own shooting setup doesn't let me use the grip shutter release very effectively unless I'm shooting a lens with focus lock buttons.
The other issue that might be important to me is AF capability with difficult dynamic subjects like birds in flight. I have always heard the D3 is better but I don't have a sense of degree. Probably just a near impossible thing to quantify.
Quick edit: I find the D700 AF to be significantly better than my D300 and very, very acceptable, perhaps remarkably good.
The 10fps would be nice too, and I have some specific subjects that would benefit from that. But not $2500 nice.
The other way I look at it is that there are a lot of lenses I could have bought with that $2500 that would do more for my shooting than the marginal benefits of the D3, and the low light performance should be about identical. The D3s is another matter and if price were viable that would be a different consideration than a "D3" verses D700.
I've never looked back on my decision and, really, throwing $5K at a body that "lasts" 4 years at most (in terms of competitive performance) is just not something I want to do. I value glass more than bodies, simply because good glass will always be good glass and is good for at least 10 years, and maybe nearly a lifetime with a little luck.
If price were no object and the ability to "slim down" without a grip was important enough, I guess I would own both . The two physical formats have advantages in different situations (for me). Neither is necessarily "superior" in a general sense.