I strongly believe that the camera you use has the smaller part to pay in the picture you take, be it Nikon or Canon they are both equally capable of taking terrible or stunning images depending who s behind it pressing the button.
I choose Canon because the lens range is just better, Nikon just don't anything as good as my 135mm f2. Maybe on paper they do, but not in your hand. And it's the lens that makes the picture. The other reason is that Canon's cameras just seem laid out in a logical fashion to me, where I have to engage the brain with the Nikon's, there are just too many buttons and this reason alone makes them pretty useless to me at weddings.
I do sometimes have people work for me who shoot Nikon, so I do get to process their RAWs, the colour reproduction is more muted but nicer and without doubt the metering and flash systems are better if you are shooting TTL. But at the end of the day both system are totally capable of offering up excellent results.
The in built flash is something that most people why buy full frame don't want. Hence it being missing from Canon's range. I wouldn't let it stop you upgrading Mark, the improved dynamic range alone would help you in situations where you use your fill flash now.
Cheers
Cris