Thing is, perry, as well-intentioned as you feel, and as real as your anecdotal experience tells you, there are people in these forums that work or have worked for MS and are deeply involved in the very file systems you're talking about. It's hard to argue against the engineers and architects who really know the underpinnings. We can devise schemes and swear by them because we feel the differences, but I've realized that the mind has a powerful way of convincing ourselves of things that run contrary to the actual ones and zeros bouncing under our fingers.
I think you should do something that could not only confirm your suspicions but would also end up in an oft-referred reference about the pros/cons of partitioning, etc:
Take a machine that you've experienced your percieved benefit. Develop an irrefutable way to benchmark it, subtracting as many variables as possible: let vista have time to index, build it's superfetch, balance, etc, for a few hours after each install.
Then install a test suite of apps, your way and then the standard way. Conduct a series of scientifict or as close to scientific tests on each setup and carefully record the results. Post them here and then this discussion could really move foward.