for me the answer is pretty easy: the better camera is the camera that has the better SYSTEM for your needs. Honestly, it is say to see how the forum deteriorate to 12 vs 16 MP, 9fps vs. 10fps and 51 points AF vs. 49 AF. Seriously, if that 4 MP/1fps or 2 points of AF is what going to make or break the shot for you, the camera body is the least of your concerns. With both cameras being so damn good (1DmkIII in canon's case and D3 in Nikon case) the camera body is the smallest part of the equation.
As some here already know, i made the full switch from a Canon 1DmkIII system to a Nikon D700/D300 system and came back to Canon after about a month. In my opinion, the Nikon cameras were better than the Canon's in almost every aspect BUT and that is a big BUT, the differences were not that great and at the end of the day, the lenses made way more of a difference and this is were Canon shines. Sure, Nikon has some lenses that seriously wipe the floor with Canon (24-70, 12-24 2.8 and the AMAZING 200-400) but due to my change in shooting subject, the Canon won at the end with its amazing primes.
again, instead of gushing over specs on a web page and hoping that the addition of 1 fps is going to make you the next Andy Rouse, take a step back and look at the entire system or better yet, go out there and actually try the competition.