I've thought about this a little more, and have boiled it down to two things...
Benchmade has better fit and finish, and better materials. My PM2 arrived with a sticky pivot due to a burr on the inner liner, and an uneven bevel grind. Granted, I only own one Spyderco, but NONE of my Benchmades needed "fixing" upon arrival.
Spyderco has better handles. By far. The reason I always carry my PM2 rather than my other knives, is the handle offers a HUGE amount of diversity as far as gripping options. The blade even has a finger choil, and the jimping is perfect. I even use the thumbhole as another way of getting even more "choked up" on the blade for greater control.
While I was reprofiling my PM2, I carried my favorite EDC Benchmade, the 943. I realized how much I valued the Spyderco every time I reached to grab the knife. The 943 handle is "slippery" compared to the PM2. Don't get me wrong, my Benchmades are beautiful knives, and marvels of engineering, but they seem to value those two qualities over being ultimately "usable".