It's hard to truly appreciate how great Metal Gear Solid 2 was until you've read James Clinton Howell's essay analyzing MGS2 and realize how much the game subconciously played with your mind.
http://www.deltaheadtranslation.com/MGS2/DOTM_TOC.htm
Seriously, after reading all that and having played every game in the series, it's hard to argue that MGS2 isn't by far the greatest game in the series.