I'm playing through them with my friend right now. Just finished 1. My plan right now is to go MGS1, MGS2, MGS4, MGRevengeance since that's always going forward in time, basically in release order, and progresses in mechanics.
Then go back to the in-universe start and go MGS3, MGS PW, MGSV. I'll probably play the MSX games and the other portable games roughly in release order after that by myself. Not sure about Twin Snakes.
MGS1 is the one to start with. It references the MSX games a bunch but it's playable without that knowledge. I'd recommend skipping the NES one entirely, it's basically a worse version of the MSX games. Any of the versions of the other games seem to be mostly fine, I'm a purist so I'm gunna' stick to the original console versions mostly though.