My vote goes to either Vagrant Story or Parasite Eve, both by SquareSoft. Both games are pretty short and I could see their stories being adapted into a 2 hour film without having to change all that much. Yeah I know Parasite Eve was originally a book and that book had a movie adaption, but I'm talking about the game's story here.
All Kojima games are crying to be movies instead, but especially Metal Gear Solid 3. Cut out the furies and just focus on The Boss, Snake, Eva, Ocelot and Volgin. I would pair it with some kind of fourth wall break during the release - like having multiple versions of the film floating around at different theaters (similar to the movie Clue) - to capture the Kojima spirit.
Oddball pick: Kerbal Space Program could be an awesome cartoon.
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MGS3 would be a big flop honestly. The story isn't that great imo. It is well executed sure, but every time I watch a MGS3 run the story is the worst part. The best part of MGS3 are the codec calls and how every is built around those calls.
I'd say MGS2 would have been a huge hit, but it is too late now because it is too contemporary, the themes are too realistic and I think most people would find it closer to conspiracy nonsense than a cautious visionary tale. The big social media platforms are literally what the Patriots wanted etc.
MGS5 story isn't that bad, the game mostly suffers from many other problems imo.
In terms of movie potential I'd rank: MGS1> Peace Walker> MGS2>MGS3>MGS5>MGS4