When I bought my first DSLR I tried out the comparable Canon and Nikon models in a shop. Although I'd never owned any equipment from either manufacturer before, I found that the Canon did everything the way I intuitively expected it to and the Nikon was bizarrely unintuitive. Even down to little things like the position of the main aperture/shutter dial - Canon's is right (for me) and Nikon's is wrong (for me).
BUT - and this is the KEY point - I know people who made exactly the same comparison and reached exactly the opposite conclusion! It's a very personal thing.
Your first DSLR is unlikely to be your last, and as they acquire lenses, flashes etc most people tend upgrade within the same system rather than switching. So the choice of system matters. Don't worry too much about whether one camera has more features than another, because in 5 years time all that will have changed anyway. But do pay attention to the ergonomics, layout, menu design etc. because these things are baked into the manufacturers' DNA and will persist for many generations of equipment.