I am no expert but I have been trying to find a solution to this very same issue for quite some time. I was using cube64 adapters and then later cube64-dx adapters to use my Gamecube wavebirds with my N64. Intercepting the controller I/O to route data back to some other device will require a hardware modification and cannot be done with the 64Drive alone.
Back in 2011 I asked darthcloud if he could perhaps integrate Memory Pak passthrough into his cube64-dx code. My idea was instead of trying to come up with a method of emulating and reading/writing Memory Pak data to an SD card, just allow the data for the Memory Pak to pass through the cube64-dx and onto a real physical Memory Pak. You could either solder it directly to the adapter or harvest a connector from a controller. This way you can use a single Memory Pak, then use the 64Drive's 'virtual' Memory Pak feature to backup those saves and have effectively unlimited storage.
Original request:
https://github.com/darthcloud/cube64-dx/issues/10 (was moved from from Google Code to GitHub back in 2015)
Unfortunately darthcloud has seems to have abandoned the project (he only took up the cube64 project from Micah who never officially released her work but did publish the code:
http://scanlime.org/2011/03/cube64-game ... 4-adaptor/) so no further work on this has been done. Perhaps eventually someone will be able to find a way to let us use Memory Paks with our Gamecube controllers without the need to swap controllers every time you need to save/load.
I started playing N64 again this fall, and made several update to Cube64.
This include the memory bypass feature
## [3.1] - 2018-02-05
### Added
- Slot bypass mode. (Fixes #10)
- GameCube joysticks scaling. (Fixes #7)
### Changed
- Ported Python2 scripts to Python3.
## [3.0] - 2018-01-03
### Added
- Support PIC18F14K22 microcontroller.
- Real-time CRC calculation. (Fixed issue #1)
- Axes remapping.
- Layout modifier function.
### Changed
- Configuration menu.
- EEPROM flexibility.
### Removed
- Support PIC12F683 microcontroller.
https://github.com/darthcloud/cube64-dx/releases
This require a new microcontroller. (PIC18F14K22)
I think the adapter is much more useful now, you can remap axis, rumble work in Banjo & golden eye & proper joystick scaling.