Starting in 1995 Nintendo included the SA1 chip in some cartridges, which was a 6502 variant running at a little over 10Mhz.
I actually think that Nintendo could have come out with a SNES Pro CD system in the mid 90s by including SA1 and SuperFX2 chips and having 4MB of RAM.
CD based systems with sprite & tile based hardware seem to have all failed due to lack of RAM. Just too memory hungry, especially once you start increasing the number of colours. The Neo Geo hardware (Motorola 68k & Z80) was able to produce hits after 2000 by using giant, expensive, cartridges.
They could have kept a 6502 based system going as a budget system (keeping the N64 as their "cadilac" system) until 2000.