The lack of 16 bit instructions isn't a big deal in many applications. I like the 65816, but you can't just drop it in "under the hood" and have 16 magic. In greenfield code you can utilize its features, but mixed with legacy code and systems you'll be changing modes more often than it is worth. Most of the code you mention would need to be significantly modified if you wanted to take advantage of the 65816's enhancements.
Sweet 16 was a vintage example of where if you need 16 bit instructions you can synthesize them on the 6502. Uzebox is a modern example of some feeling 8 bits is enough for gaming.
The Mega 65 is exactly what it claims to be--the realization of Commodore's unfinished 8 bit succesor. It blazes when you compare it to the Spectrum Next that is in development with a selectable 3.5 or 7 MHz Z80 core. And as much as I love the 6502, the 6809 would be a tempting direction to move to 16 bits.