I think it was one of the first games to give you choices in this genre, like you get a boat load of guns but are rewarded for not using them. With the prison scene there are a few ways to get out, one of which being to use tomato ketchup to look like blood to get the guard to come in.
I think it was the first game to let you snap on to a wall and take peak round the corner.
The plot is much better than your average "something wants to take over the world and it must be stopped", mainly 'cos they already have taken over the world ...
The characters are freaking awesome, boss letting herself be branded a traitor and hated by the country she loved, that she died for.
It (at times) doesn't take it's elf too seriously, either by codec messages or being able to kiss a poster, being able to lay on your back on a bed and stir at a poster of a Japanese model that refills your psych gauge, to Johnny having the shits all the time and hiding in a box to sneak around.
There is also lots of hidden extras, like in the first one if you crawl through a shaft a number of times you can see a girl doing exercises in her underwear (she starts them off dressed).
The games are always REALLY hard, on easy there an absolute cake walk but on the hardest setting on MGS4 they can smell you ...