I think vortex generators are a great idea, and I've often thought of trying them myself.
A lot of people don't realize that the rear of a vehicle is at least as important as the front, aerodynamically speaking. Splitting the airstream in half cleanly is important, but it's equally important to bring it back together cleanly after the vehicle has passed through. If you don't, you'll get huge vortices and partial vacuums which will consume tremendous amounts of energy -- they create drag.
Vortex generators add just enough movement to the airstream that it's better able to merge together after the vehicle has passed. You're basically adding a bit of drag in order to save more. So they're very sensitive to placement, size and shape, and you'll need to do a fair amount of playing around to get the best configuration. It will also be difficult to determine in the real world when you've really made an improvement, unless you happen to have a wind tunnel handy. But I still think it's a great idea.