The NES took the 6502 design and coupled it with some audio logic for their custom CPU. The GPU is off to the lower left on the NES board.
6502 chips were everywhere back in the NES heydey. They had a fairly straightforward instruction set as well as pretty good support for sprites and other things you'd want to get Mega Man to jump. There were also a few "undocumented" instructions. It wasn't anything sneaky, their behavior just wasn't defined, but the chip still accepted them. Some clever people found ways to use them to make their code faster which is pretty astounding.
These days chips need to be designed with large amounts of computer aid, but these were more or less laid out on graph paper and then put into production. Life was simpler then, but -- to be honest -- the original Metal Gear is no where near as fun as the latest.
More history and archeology ahoy: