Well, I guess every company has stupid foibles in their system.
Nikon is obsessed with forward and backward compatibility (which isn't always a bad thing, but it's only for their more expensive, high-end gear), but this means that the lens mount is still full of mechanical couplings. They seem to cripple their metering system by making it dependent on the lens to communicate information. There's a plethora of what lenses will work fully, partially or at all on what bodies. With Canon, EOS is EOS is EOS (which the exception of EF-S lenses on an EF body, but who would want to do that anyway?) and the couplings are completely electronic. Canon's metering is also lens-independent.
On the other hand, rear-curtain flash sync (which I use all the time) on a Canon requires eTTL communication between the body and flash. Nikon just pops the "fire" signal at end of the exposure. This means you can't use affordable-but-perfectly-good alternative products (Vivitar flashes, Alienbees Cybersyncs) to their full potential. Holding a Canon feels like holding a brick; Nikon bodies are crafted by Giorgetto Giugiaro and seem fit your hands, no matter what size they are (seriously, I'm comfortable holding everything from a D40 to D3). Canon has long-winded, disorganized custom function menus that sometimes require referencing the manual (seriously? The 1980's called, they want their functionality back). Nikon's menus are organized, clearly-labeled and just seem to always be exactly where you'd expect to find them.