I think that people vastly underestimate the gameplay of the MGS series for a few reasons:
1. The cutscenes, they sort of break up the gameplay so you typically aren't playing for more than 20 minutes until you run into another story sequence.
2. The silenced tranq gun is overpowered, why would you use all the gadgets and weapons when you just use a headshot from the hushpuppy to instantly subdue every enemy. In MGS2 and 3 you can shoot out enemy radios, shoot there knees to slow there movement, shoot there arms to prevent them form firing guns, and hold guards up and use CQC to perform dozens of other actions. The games give too many supplies to the player so you really don't have to get that creative. You could capture a poisonous snake to throw at guards but that's impractical if you can just shoot a guy.
3. the games introduce mechanics never to use them ever again. In MGS 1 there is one area where your foot prints are detected in the snow, in 2 there are a few areas where steam pipes can KO enemies. There are a few times where guards will notice the water you left on the floor for being drenched in the rain.
I strongly recommend people to try out the VR missions in 1 and 2, they actually give you scenarios where the depth of these games shine. While the controls in the game are a little clunky, they do have uses and the games have an insane amount of detail in how the player can interact with the environment and enemies. MGS1 is the most archaic of these games, but I would not say it aged poorly, especially compared to other games released in 1998.
I also strongly recommend people to watch the superbunnyhop and matthewmatosis reviews for these games. They are incredibly insightful.