Hack the guts of a Wavebird (or similar) into an empty N64 controller shell? Space would definately be an issue so any boards inside are going to be shoehorned in. Miniature cherries? Meh,

You'll probably lose any functionality from the controller port, which is just as well, you need some place to put the battery. I can't recall which of the addon peripherals for that slot sport batteries without hacking them apart as well.