This w/ mods VS GOG version with mods

[Sammo]

I have the GOG version already but which would be considered the better experience?

[Deathraven13]

Does the GOG version allow you to aim with L3 ? If not then MGS2 from this collection is better.

[neon.wir]

The Master Collection version has some unique issues. Bad audio levels, incorrect sound effects, and various other bugs. Barring things like crashes or framerate issues, which more than a few experience, it should play fine overall. If you want better quality audio and resolutions above 720p and other niceties, you will want to check out the essential mods thread here:
https://steamcommunity.com/app/2131640/discussions/0/3935643263185640453/

The older PC port, if playing the GOG release, should "work" but will not be optimized for a modern setup. To get it running in widescreen, improved controller support, and other options you will want something called V's Fix and you should be good to go. This version also has a trainer which is great for practicing if you ever want to go for something like Big Boss rank, as well as the SOS mod to give it a 3D camera like in Snake Eater.

Neither of them are particularly ideal. Running each "out of the box" then the Master Collection version is better. But I'd say the GOG version you have edges out the Master Collection release provided you run it with V's fix.