WARNING: This entire post contains spoilers for those that haven't beaten Metal Gear Solid 4!!!
In my opinion, the story was the best simply ebcause the plot twists were at least as big as any other of the games, and the characters were even more real this time. In terms of characterization, MGS4 wins hands down.
The Beast bosses shows that he's a pervert... how? :S just because some boss here or there got molested or whatever doesn't make him a perverted. Shit like that happens in real life, and I for one am glad that Konami didn't shy away from including stuff like that. It happens here, it happens in the game.
The bosses from MGS2 were far from masterpieces. Fortune was VERY generic, aside from her "you can't-shoot-me" madskillz, Fatman was so-so, nothing particularly special about him, and Vamp made a return in MGS4 so equal brilliance there.
The boss fight between Rex and Ray in MGS4 is EPIC. Claim otherwise and you're NUTS. That entire scenario was like a wet dream! The beasts were mostly fun, though some (like Raven) were annoying. That first one, the stealthy one, was quite fun, IMO. Snake VS Liquid was also cool ^_^
The game makes it clear that you can stealth your way through things, and shoot your way through things. I used a combination of both. Another nice point in MGS4 since half of the time, it really was easier to simply sneak by rather than shoot. It's part of the story that warfare is routine, more open, and more controlled. Not stealthing through anything was fine with me
The fourth was the best in my opinion, best story, best gameplay and awesome mecha fight
First I was disappointed that Snake didn't kill himself because that would've been a great ending in my opinion (either that, or that he died getting fried up). But, the plot twist at the end (BIG BOSS IS BLEEPING ALIVE!!!) kind of makes up for it =)