Another consideration that seems to be overlooked a lot is simply the feel of a camera.
When upgrading from my old Konica Minolta (rip) gear before the new Sonys were available, I gave myself two options, a full Nikon kit and a full Canon kit (based on quality and quantity of lenses available).
So I went to camera stores and I handled them, and within my budget managed to work down to one or two available bodies and properly tried those.
In the end the Canon 40D just sat a lot better with me (only after the addition of a battery grip) than any equivalent Nikon did, and given the amount of time using the camera, it was possibly the most important decision to make. I can still walk around all day with the body/grip, 70-200 2.8L IS and flash without feeling any kind of discomfort or fatigue in my hands, something that the Nikons managed after only a relatively short period of time.
Of course, this changes when housings come into play, but for people who use their cameras above water as well as below, I still think it's a fairly important point.
P.S. fwiw I still shoot with my 40D after what seems like an age in the upgrade world and would only consider adding more lenses until the body dies, and only then will a new body be considered. So long as it feels right...