Small update on the state of this project:
As of my previous update, the console was 100% built and I was working on building additional cartridges. I had 18 carts built and have been working on one final (at least for now) cartridge that comes with a few additional features. I'm excited to show this one off, but that will come soon enough.
Suffice it to say, while working on this final cart, I thought it was done, but I had a stray ground that shorted and caused the arduino board to wig out a bit. I'm almost absolutely certain I've fixed the problem in the cartridge, but the damage is done and the arduino is mildly jacked up; it's sending some unwanted button presses through the carts, which makes some games unplayable and keep others from booting at all.
The fix should be easy enough; I've ordered a new arduino clone and it should just be a matter of uploading the finished controller code and rewiring the connections. Once that's finished, I'll start work on a completion vid.
Edit: New arduino clone came in and I wired it up and programmed it... same issue. I pulled all the wires off of the board and the console and figured I'd start from square one, in terms of wiring. Started by connecting the controller port and confirming that the serial console was reporting the correct buttons were being pressed. That worked, so I moved on to wiring a few buttons to the cart slot, testing, adding a few more, etc.
Finally, everything is wired up correctly again, but something strange has happened: a few of the plug-n-plays relied on 6V (4x AA batteries), but they ran just fine on the 5V being supplied by the arduino before I screwed the pooch a few days ago. Now that doesn't seem to be the case. Some power on but video quickly shuts off, some have graphical glitches. I'm not sure why they're behaving any differently. It's as if the arduino previously fed out 5.5V and now it's a hardline 5. If I never figure this out, I guess I'll just have a few unplayable cartridges.