Remember when you input your data into the computer terminal during MGS2, and at the end of the game Raiden pulls out his dogtags with all that info (your info) on it? There's good reason for that. Like I said, Raiden represents you, the player. Or at least he does up to a point.
Raiden was "bishounen" to appeal to both sexes. He's also a child-soldier, trained by Solidus in previous wars. Translated, that is the equivalent of us (most of us) being child-gamers and having experience with Metal Gear, MGS, and video games in general.
When you first use Raiden, he tries to be Snake, just as you have played Snake's role all along. When it comes down to it, however, he just isn't Snake. Like you, he will never be Snake. That's why everything he does while assuming this role is either a failure or is done in vain. I see Raiden's tortured nude scene as a representation of the vulnerability and the stripping-down (sorry for the pun) of this charade of "being Snake."
Raiden finally finds his identity after taking Olga's sword and learning that he is being manipulated by the Patriots. At this point, Raiden and Kojima leave us in the dust. Raiden now knows more than we do; he ascends beyond the player and our wanting to play Snake's role.
When we are playing MGS4 as Snake, Snake has some very close calls and near death experiences. As players, we fear for the worst, and anxiously hope for relief. We think: "how can Snake die? There must be something I can do!" And then Raiden comes to the rescue. Raiden represents us and what we would do. This time, however, he really represents the player, and not the player as Snake. As MGS4 goes on and Solid Snake gets older and more vulnerable, we begin to fall out of his identity and his role. At the end, you are immersed in the story from your own perspective instead of Snake's. Raiden is the key for us to be us and not merely a character, and so we evolve just as Raiden evolved.
When the patriots and their actions are revealed, it makes us question what and who is really right or wrong and good or evil. It makes us too feel used by the Patriots for playing Snake's role when Snake has been used by them all along. In the end, everyone either dies or is set free from the events. It is thanks to Raiden's brilliant character design that we too can have closure and be free from this story and our attachments. Just like Raiden took off and returned to peace, we can explore other games and stories (and ourselves as individuals), and have our own peace with ourselves and with the Metal Gear series.