Nikon's 600mm is still the old version I lens, which is very similar to Canon's MkI. Canon's MkII is optically better, and the Nikon I weighs 30% more. Unlike the MkI versions of both, Canon's 600 II is actually handholdable. To me, at least, that's worth a big premium.
Relative to the version 1 Canon the Nikon 600mm is much much newer. The Nikon was announced on Aug 23, 2007 while the version 1 Canon was announced September 1999. A 8 year gap between the two 600mm.
I am using the Nikon price as a gauge whether the current Canon 600mm (announced Feb 7, 2011) is a bargain to buy already. Bargain being a relative term of course.
The current 600mm is $13,000 so when it drops nearing $10,300 then it is a great time to buy a "want".
Now if you "need" a 600mm today I would strongly consider the Canon for the technical aspects you pointed out. But alas the current 600mm is perpetually out of stock in most places so you may want to consider looking at other focal lengths to get to where you want.