Metal Gear for me is separated into faves and what I consider the best.
MGS1 is my favorite due to its setting, the fact it has the best enemies in the series, the storyline, and voice acting. It has MG cheese and silliness but is done in the best manner possible. On the other hand certain elements of it have aged such as the shooting and some of the boss fights were better represented in future games. But it's by far my favorite.
I think Metal Gear Solid 2 Substance (not original) is the best game in the series. The inclusion of features European Extreme, all the new modes, dog tags, VR missions, add a dynamic to the game that made it the most replayable in the series for me. It has the hardcore MGS gameplay without feeling slow like MGS3. It strikes a perfect balance in terms of gameplay for me and its main flaw is that the story, setting, and enemies aren't the best. But that gameplay.
On the other hand MGS3 is superb, especially Subsistence. It'd probably be what I consider the best of it weren't so slow. Always scouting for enemies, the lack of radar, healing yourself, the camo stuff. I think objectively it has the best gameplay in the series but I don't find it the funnest to play, if that makes any sense? The bosses not having back stories takes this game down a notch too but it has the best overall story in a MG game so it has that going for it. The End is my favorite boss fight of all time. If it had VR missions I think it'd be the best MG game but it doesn't. Fuck MGO!
MGS2S > MGS3S > MGS3 > MGS1 > MGS2 > MG2 > GZ> GB > Twin Snakes > MGSV > MG1 > MGS4