This game, in a word, is masterful. Every aspect of this game is well done. The story, while difficult to follow at times, is awesome, full plot twists and emotional moments. The ending in particular has the story transform in ways you would never imagine. The music is just outstanding, namely the main theme and the boss battle music. The gameplay takes everything good about the original Metal Gear Solid and just beefs it up to a whole new level. The stealth aspects in particular have evolved exceptionally well. In particular, the ability to hold people up at gunpoint is awesome.
The biggest complaint with this game is that you don't play as Solid Snake for the majority of it, but rather you play as Raiden. In truth, I really like Raiden as the protagonist. It allows the story center around him and his back story, which allows for more variation in the story. Granted, he's not as cool as Snake, but he's no issue.

This game is a must play for anyone. It truly is a masterpiece.