GOG brought joy to many Metal Gear fans after announcing that MGS and MGS 2: Substance released on the platform. However, the rough nature of the ports and their controls requires some work for proper enjoyment.
Metal Gear Solid and Metal Gear Solid 2: Sons of Liberty PC versions have always been problematic when it comes to controller compatibility. Some of the biggest issues ranged from not being able to map triggers to Xbox controllers to absolute inability to use DualShock ones.
Direct input usually yielded the best results but that wasn't always an option. Furthermore, keyboard controls are pretty messy and they definitely subtract from the games' potential to be enjoyed.
Thankfully, the community came up with ways to bypass these issues in the past. First of all, there is the solution for Xinput woes, or in other words - the way to fix the game enough to be able to use Xbox controllers properly . There is also 1080p support included in the fix to boot.
Besides that pile of fixes, you can also check out V's Fix which will help with Xbox Controller issues in a similar manner. The main difference is that this one will bring around the support for DualShock controllers as well.
To make sure the fix works, read the provided text document that will help you install properly.
In the case of V's Fix, there is a whole block of text that describes the additional features, such as support for widescreen resolutions and more.