In the case of the D4 vs D800, this has perplexed many including me, until I gave it some real thought. I struggled deciding which to buy, until I really started to dig into it a bit. The D4 is well known as a world class tool for photographing sports (my business), but the D800 offered a number of items that you point out at a lower cost.
In the end for me, the real deal breaker for the D4 was it's overall feel, durability, exceptional low light performance, buffer size, and speed. Granted the D800 is close on many of these, but the D4 felt to me like a more "workhorse" type camera that could suit my needs for many, many years to come. I do not like buying cameras (they cost too much) so if I can buy one to last me a really long time, it's a good thing. My D3 is a great example of that.