One of the things that I'm curious about: How easy / hard is it to use the same NES game with higher resolution / color graphics, and sample-based sound?
Are there any emulators out there that let you swap in higher resolution assets so a game can be freshened without a complete port?
I would not think so, at least not in a meaningful way. That would require to edit the cartridge data thus the ROM, as all sprite data was contained within the cartridge. Sample based sound is impossible natively, as NES and older game consoles don't work with digital data but synthesizers. You could perhaps synthesize the music to WAV files and then enchance it. But then again, NES and thus its emulators have no way of playing digitized audio!
The NES in particular is probably not too difficult to upscale, because the graphics data is stored on its own ROM chip (sometimes RAM) in a well structured layout. SMB1 just uses a ROM chip containing many tile graphics which the CPU code addresses by tile index. It would be really easy for an emulator to use the same tile indices to address any arbitrary set of tiles loaded from a PNG. Some games use RAM, which makes it harder as you'd have to index the PNG by hash or something.