@Dex One of my friends took the matter into his own hands 5 years back by building a contraption based around an Arduino, N64 controller and a Transfer Pak, which certainly sounds like a lot fewer pins to worry about than normal.
@NovaSquirrel (From some further searching it turns out that the Game Boy Interface GC homebrew can dump ROMs from the GB Player as well - though not sure if it can do saves, which is the important part to me... or would have been)
@NovaSquirrel I did wonder earlier if someone had created some GC homebrew that could dump them out using the GB Player.
Looking it up:
There's some GC/Wii homebrew that can dump GBA games/saves over the GC-to-GBA cable (though this takes a very long time), and DS slot flashcards have been able to do that for a while.
For GB/GBC games, apparently there's been an app around for the EverDrive 64 for a while that can also dump via Transfer Pak - though the Arduino is probably cheaper.