Matthew:
I think you have a lot going for you in the implementation of the VDP in a gate array. Its a lot like Thierry's IDE card and USB card projects. As an old 99'er from way back, I think your premise of staying as close to what's under the hood of a regular black and silver console makes sense. There aren't that many 99'ers who have a PEB or the means to get one and your project makes it not only affordable (at the proposed $80 US price point), but desirable. I further agree with you in being able to pop a cartridge in the console and run "barefooted" is a great way to test compatibility. I eagerly await the results here in the great NorthWet.
Rick