I prefer SC because of the fantastic gameplay (at least in 1 & 3, that is) and the downright badassness of the game.
MGS has its plusses, though. Even though I think Kojima is a story hack, the amount of polish and work put into the games is truly phenomenal.
Overall, they're both fun games for very different reasons. SC is a better straight-up stealth game while MGS has its share of fun quirks and pretty amazing game moments.

Or check out my new webcomic: http://selfcentent.com/







