The problem is many/most NES carts have additional circuitry (termed mappers) for bankswitching chunks of ROM in and out of the normal address spaces. The NES also has two address & data buses (CPU and GPU), which would probably make flash carts more difficult.
Then there's the NES lockout chip, although it can be bypassed by modifying the console. But the big N has a rep for strongly protecting it's IP.