Don't buy beginner Nikon cameras like the D3000 or D5000 and expect to use dedicated, professional, prime lenses like the 85,105,135,180mm primes or the old-school wide-angle primes...if you want a NIKON, buy a NIKON, like a D90, D300s, D700, or D3s. Problem solved.
If you want more megapixels, Canon will deliver higher MP counts as long as consumers want higher MP counts. Even if it means that most of their consumer lenses are not up to the task of imaging to a smaller, higher-density sensor. The higher MP count of say the 7D verus the D300s doesn't really show up much,since the higher MP count sensor pushes the lens's recording farther down on the MTF curve of every lens you mount, so the 7D ends up with lower color saturation and lower contrast that lower-density sensor camera from Canon,Sony,and Nikon...
The full-frame sensor cameras are till going to out-perform the crop-body cameras at elevated ISO settings...Currently Cano has no mid-line action/sports camera that's Full Frame that can compete with the D700 or D3s for sports/PJ/low-light work...with Canon the 5D series is crappy AF and average light metering,no flash,no flash commander, and 3.9 FPS, but good video...Nikon has the D700 with pro AF, fast speed, and pro features like flash commander and built-in flash for triggering slaves...
Nikon has better ergonomics in terms of AF point navigation, better AUTO ISO (Canon STILL will not create an AUTO ISO system that allows people to use it like Nikon or Pentax) setup, and Nikon has on balance, better light metering in more cameras, as well as the same,dedicated shutter and aperture controls in different camera modes--Canon;s yo-yo back and forth,back and forth, so the aperture and shutter controls shift back and forth between the front wheel and the back wheel, willy-nilly. The cameras are very different,ergonomically.