The main issue is being willing to sacrifice the controllers. I considered having switches (or relays, or a software equivalent) to switch controllers from "host" to "slave" modes, but that would require a ton of extra wires inside the controllers. Probably too many to be able to close them back up and still have them be functional/comfortable. I still might try that on a Genesis controller, since the 3-button controllers are huge and have plenty of space inside them for extra stuff. But since that's not going to be the case for most of these controllers, I figure I'll have a "controller box" with the PCBs of each controller in it. And two different "input" connectors. An HDMI connector for Atari 2600, NES, Genesis, SNES, 3DO, PS1*, N64, and Dreamcast. A DVI-I connector for PS2, Xbox, Gamecube, Wii classic controller, Xbox 360**, and PS3.
As far as the joysticks, I'm doing to them basically the same thing I'm doing with the buttons. In this case, desoldering the analog sticks, and soldering wires to the connector. Most gamepad analog sticks use 10k potentiometers, though IIRC some use 5k. Any that are different, I can make up the difference with resistors. The same if extending them that far messes with their resistance. I'll probably have to correct for that, too. With the N64, I will likely use a Superpad (third party) since it uses standard analog sticks and not that crazy one Nintendo put on the stock N64 controller. Granted, there are mods you can do to the original Nintendo controllers to make them accept normal analog sticks, but it'd just be easier to use a third party controller.
Another obstacle is needing controllers which use a "common ground" for all the buttons. In some cases, I will need to use the PCBs from third party controllers here as well.
I know it's a crazy ambitious project, but for the time being, I'm mostly focused on getting my arcade stick to work on the 3DO and Genesis, and getting my 360 controller to work on PS2. But by starting out with having a common pinout (and connectors) for all of these, it will make future mods easier and immediately compatible. I'm not new to these kinds of controller mods, either. I mean, I built this big dumb beast
a few years ago, along with a portable PS1, portable PS2, a GBA with bigger backlit screen, and a portable NES.*I'm only aware of ONE game on the PSX that actually requires analog sticks, that being Ape Escape. Pretty much every other game works perfectly on a D-pad. Even games that could use the analog sticks were required by Sony to be fully playable on the D-pad. Ape Escape itself being published internally by Sony and used as a demonstration for their analog sticks. Hypocrites.
**The 360 controller will also have a switch to switch the USB between the 360 and my PC.