I don't see why it has to be exclusive one way or the other. MAME is going to be the best option for a lot of arcade games (aside from real PCB's), but there are plenty of great console exclusives.
A few options:
1. Run the button wiring through a switch to select which platform's controller/encoder is connected to the buttons.
2. Wire to both encoders in common ground, with a switch to ensure only one platform is powering and communicating with them at once.
3. Use an encoder compatible with multiple platforms, with a switch to ensure only one platform is powering and communicating with it at once.
This can be done easily just by running the right wires to a dsub switchbox. Depending on how many buttons you're using you could probably fit everything on one switch, like a db-25 or db-37, or you could use one for A/V and one for controls.
If you're a little more tech savvy, you could build a custom switching circuit using solid state relays, like a 4066 chip.