Yeah, depends on the intended use. But one thing I have found: the flagship-level bodies have much faster response time and latency time than the lower-level bodies. The 1D series Canon bodies are faster in operation; the 5D is actually pretty slow by comparison. You'll see this most in action work. With a slow body like a 5D, you have to press the shutter release button as the field goal kicker's leg comes to the back of the swing...with a faster, professional-level body, the needed allowance for the mirror to swing up is much,much shorter. These types of things are measured in milliseconds, but the 5D is somewhere around twice as slow I would say, as the 1D III is in terms of shutter lag, and in how fast the mirror comes back down and brings back the viewing image. PLus, if you add in the frame rate differences, which is another matter entirely, then the overall speed advantage of the pro-level bodies really begins to be compounded. People who have not owned or extensively used a pro-level body will sometimes tend to dismiss these types of issues, but they are very real in actual photography on a day-by-day-by-day type basis.
You might find that you "shoot better" with what is by specifications, a "lesser" camera in terms of megapixel count, but a much,much higher level of camera-building and engineering underlying it. There is a reason the flagship camera bodies cost more than the mid-level bodies, and much of it has to do with the absolute speed and responsiveness of the mechanics, as well as viewfinder system and pentaprism quality and clarity.