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This version of the game actually has fewer visual bugs than the 2011 HD Collection version.
I recommend MGSHDFix to play at any resolution you want, rather than having to resort to upscaling if you play at resolutions higher than 1080p. The Better Audio mod is also a necessity for me. There are quite a few more great mods that fix more issues that were introduced in the HD Collection, but I'll let you decide which version to play first.
For reference, if you're worried about missing content, there really isn't any. The only thing not here from the 2002 Substance release on PS2 is the skateboarding mini game, but this was really just a demo for Konami's then upcoming Evolution Skateboarding game, which ran on a completely different engine and to be honest wasn't very good.
Other than that, all content from Substance is here and accounted for.
Story wise, gameplay wise, they're all much of a muchness between the versions. The PS3 port has slowdown issues with a couple of boss fights that the Master Collection just doesn't have.
I'd not bother with the ps3 unless you plan on playing games that are ps3 exclusive. Not now. Unless you're already a fan of the series and want to play all the mainline games. If you're a casual player who is new to the series then just get the Master Collection.
There is a PC port of MGS2 Substance 2002 which you can find on the 2nd hand market. This needs mods to play.
The Master Collection on Steam with fan made bugfix mods, especially after patch 2.0.0 which released in October (adding proper 4K support, upscaled all the videos up to 4K, added keyboard/mouse & controller rebinding, ect) - is definitely the definitive way to play MGS2 & MGS3 nowadays.
Ontop of the higher resolution support/4k upscaled videos/additional remastered textures, ect, there's over 62 bugs that have been fixed from the PS3/X360 collection versions (that are currently identified.) https://docs.google.com/spreadsheets/d/1WhQSRpkC_A9wBDV0o-Pohh1dMhL1H6nbVzvdluIVWrw/edit?gid=1495630081#gid=1495630081
Likewise, there's mods for the MC that restore a bunch of content that got censored as well as music tracks that got cut from multiple cutscenes in all releases that came after the original 2001 PS2 Sons of Liberty release (meaning even the PS2 version of Substance was ALSO censored & had cut content) - https://www.nexusmods.com/metalgearsolid2mc/mods/15
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As for the PS2 version, there was a promotional crossover demo with a game called evolution skateboarding that got cut from the HDC & MC (due to the demo running in a completely different game engine for an old PS2 game). Otherwise, the MC is the superior version in every way (with restoration mods.)
Again, the same caveat about emulation applies with MGS2 as well; the PS2 versions are only good if playing on a PS2 with an actual CRT.
For example, while emulating via PCSX2, cutscene fade transitions (which are done through a render to texture technique - for example during the first fortune encounter) still only render at native PS2 resolution[imgur.com], and a couple cutscenes can outright break and force you to skip them to continue playing. There's more bugs on their wiki here too; https://wiki.pcsx2.net/Metal_Gear_Solid_2:_Substance#Known_Issues
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Here's my Bugfix modpacks that fix a bunch of issues still present in version 2.0.1 ranging from pillarboxing issue, invisible textures, audio compression issues, broken water reflections, crashing during cutscenes, ECT - issues that have been present since 2002 in most cases. They also restore a bunch of censored content[www.movie-censorship.com].
MG1 / MG2SS (MGSHDFix, adds native 4k internal render resolution & ultra-widescreen support.)
https://www.nexusmods.com/metalgearandmetalgear2mc/mods/9
MGS2 (My bugfix modpack with all the bugfix mods, including MGSHDFix & Better Audio, preconfigured so it's only one click to install everything via vortex mod manager):
MGS3 (Same as above. All the bugfix mods preconfigured for one click install via vortex mod manager):
Bonus Content aka MG1/MG2 NES (MGSM2Fix - Adds 1440p/4k internal render resolution & ultra-widescreen support, and romhack loading.)
https://www.nexusmods.com/metalgearsolidmc/mods/5