Metal Gear, in my opinion, resembles an RPG more than a shoot-em-up game. Metal Gear, in many cases, avoids shooting mass numbers of enemies entirely. I mean, how many shooters have a cardboard box for their hero to hide inside of?

How Metal Gear resembles an RPG
The story of each game in the series directly involves the player. While shooters, have little story, Metal Gear has an evolving story. RPGs tend to have a player follow linear storyline, but with multiple choices on how to get there. Metal Gear follows this idea in that many situations can be handled in multiple ways or routes. Where in a shooter you had the choice of blasting your way in or dying, Metal Gear allows the option of sneaking in, distracting enemies, or quietly disposing of foes. Metal Gear force the player to have a small emotional attachment to Solid Snake and other characters of the game throughout his actions the story. You hate the enemies, even the brand x baddies for their cruel actions towards the hero and his allies.

Like RPGs, Metal Gear has character evolution. Traditionally, role-playing games have a ranking system for characters to progress along as the story continues. Likewise, metal gear has a ranking system where Snake can level up his stats. RPGs have a character's hit points increase, Metal Gear has a growing life bar. RPGs have power levels, Metal Gear has guns. Potions, rations. Level restrictions, key cards. And so on. Certain item in RPGs allow the character progress further into the world they are fighting in. This is mirrored in metal gear with key cards, ropes, and explosives. Having Solid Snake use C4 to blow down a door to the computer room is much less geekier than using a magical elvish item to gain entrance to the cave of wisdom. Barriers, such as a locked door, present a challenge to evolve a character but in a different way. Where in other RPGs a level 10 wizard is the only way to cast a spell to open a door, Metal Gear has Solid Snake hold a level 3 key card to open a door.

How Metal Gear is a shooter
There are guns, lots of guns. Although guns increase in power as levels proceed, this happens in most shooters. Also, Snake is a killer, he does this well and there is not an emotional attachment that tears at you when he loses against a boss or even a smaller battle. Instead, you hit continue and make your way back to that point. Although Snake's goal is to avoid contact with enemies, in many cases killing is highly stressed (mostly when you trip an alarm and a swarm of enemies must be disposed of). I think, Metal Gear could best be classified as a "Cool alternative to an RPG". Not to say that Final Fantasy is poorly done, it is great. But, guys play computer games, and Metal Gear is far more macho than Princess Maker 2.