drdouchebag: MGS 2 doesn't seem to be recognizing my Bluetooth Xbox controller on PC. Why? How to fix?
WaywardPooch: This is a re-release of the PC port from long ago! As such, X-Input controllers and widescreen monitors didn't exist yet, so it doesn't surprise me that they don't work well here out of the box.
Thankfully, that also means fan-made patches from "long ago" still work with this version of the game.
The best one I could find was V's Patch, which you can download from GitHub using this link.
You basically just copy it to the "bin" folder within the game installation folder, then run it like a normal program. It'll let you correctly set graphic settings and pick from various controller layouts (xbox and playstation controllers included).
Hope this helps: ran into the same issue this morning.