Thanks for the tip on using EVR. My Core 2 Duo e6850 3.0 has no problem decoding 1080p/720p .TS/.MKV files using the "System Default" option(which does not shut off Aero either, only the "Overlay Mixer" option seems to do this). But if I can offload more video decoding instructions to the GPU I'm all for it(ideologically speaking, that's what high-end GPUs should be doing IMO).
Also, I recently bought Left 4 Dead 2, and have it running in a "borderless window" mode(which some apps call "fake fullscreen" - i.e. it looks the same as full-screen but is actually using a window which takes up the entire monitor) - WITH Aero. I can tell Aero is running by using the (Windows key+Tab) "Aero Flip", which is only available while Aero is running. I can even bring up the transparent task-bar/start menu using alt-tab and "Aero Flip", and see the transparent Aero effect in the game behind it, further proof that the game is running with Aero simultaneously.
For all intents and purposes my problem is now solved, I have the latest Source Engine games and Hi-Def .TS and .MKV files running without Aero ever shutting off - exactly how I wanted it from the beginning, and how I had my copy of Vista Business x64 working.
Thanks for the help and tips, especially the ones on using the MPC options.