One is that the Nikon has better strobe support for TTL,
This may be a little misleading to someone who isn't totally into all the tech stuff - there are plentiful choices for strobes for pretty much all dslrs...no matter the manufacturer. This wouldn't even make my top ten list of things to think about, personally.
Whoever suggested you head into a store and try them out for yourself was spot on (Prious, I think - his whole post was great). There are differences between brands and models other than things you'll be able to "feel" but are they differences most of the real life people on the planet will notice? Not really This is a good thing coz as long as you narrow it down to a couple of choices (check housing support!) and go from there you'll end up with a system that works for YOU.