Part 3: Snake is Old
PART 4: Raiden is Cyborg Ninja
At the end of Metal Gear Solid 2, we see Raiden throwing away his old ID tags, inspired to start his life again and embrace his responsibilities for the first time. Here's what he says to Rose:
Jack: Yeah. But genes aren't the only thing you pass on. There are too many things that aren't written into our DNA. It's up to us to teach that to our children.
Rose: What kind of things?
Jack: About the environment, our ideas, our culture... poetry... compassion... sorrow... joy... We'll tell them everything... together.
Rose: Is that a -- proposal?
Jack: This is for your ears -- only...
And yet, a few years later, we see that Raiden is a cyborg-ninja wannabe who left his family and roamed the earth in order to become a bona fide badass... at least that's the idea. The question is why Kojima would reverse the direction he was clearly going in with Raiden, and what it means.
Obvious Reasons
Why is Raiden a cyborg ninja? The easy answer is that Kojima wanted to flip people's negative opinions of him. He even went so far as to promise that fans would love him by the end of the game.* The best way to accomplish this feat was to make him an imitation of Cyborg Ninja. Instant popularity!
Storywise, the reason for Raiden's transformation requires detective work to piece together, but apparently goes like this: following the Big Shell incident, Raiden hooks up with Rose but eventually becomes emo and leaves her. He then searches for Sunny, somehow meeting Big Mama in the process. She offers to give him Sunny's location, but only in exchange for the data on Big Boss' remains... Data that he somehow obtained from GW... With this information they manage to rescue Sunny, dump her off with Snake, and proceed to take Big Boss' (actually Solidus') remains from the Patriots. During this attempt he is captured and experimented on, being turned into the new Gray Fox. He's rescued by Big Mama eventually, deciding it would be best to wander the earth and learn how to be a ninja properly. This is as generous and inclusive an understanding as you can get.
The parallels to Gray Fox are everywhere, too. Aside from his appearance and skills, Raiden ends up calling Snake out of the blue to give him advice, saving his life repeatedly, rescuing and taking care of a little girl who turns out to be a genius scientist, loses his arm, and making a self-sacrificing last stand against the enemy's final weapon. Of course this is all coincidental in story terms.
With his reputation boosted and his future bright, Raiden is poised to take the lead role in the next Metal Gear game. What better reason could you have for turning him into a Cyborg Ninja?
The Hidden Reasons
Remember how in Sons of Liberty Raiden was supposedto represent the player? It's no unforseen accident that he became unpopular. Kojima wanted 
to leave the series on a question mark, forcing players to examine and re-examine the game from every angle, until they found the deeper messages hidden between the lines. But, unfortunately for him, he overestimated the intelligence of his fanbase and consequently met with irresistible pressure to answer the unanswerable; to solve his own paradox. This is where Raiden's transformation—like Solid Snake's—becomes iconic.
Instead of listening to the advice of Snake, Raiden continued to allow his past to haunt him and determine his future. He didn't take a new name, start over, or see Rose for what she was. Likewise, players refused to give MGS2 a second chance and find the deeper meanings; in this sense, Raiden still represents the player. Snake puts it this way:
Snake: Raiden... Five years ago... That's not what I meant.
This directly echoes the sentiments of Kojima himself in an interview about the theme of "Sense":
"...I began to wonder if my message of what we should pass on to future generations had truly gotten through, both to players and my team..."
In both the game and the interview, Kojima is telling people that they've failed to understand the "sense" of the series. But rather than blame everyone for being "unfit to decide" (as the Patriots A.I. do toward the end of MGS2), he takes the blame on his own shoulders...
"However, it hit me that maybe there are some things you can't pass on. A person's will, thoughts, and emotions aren't encoded into their genes, and they aren't a part of memes either. If you group together those remaining factors, you're left with a person's sense, and that's the theme of the game this time around."
Seeing that his preaching was in vain, Kojima gave up on enlightening the players (like Snake gave up on Philanthropy,) and simply let Raiden become a badass killing machine with a big manly dick. Awesome!
Sacrificing his personality as well as his duty to family, Raiden is shallow and over-the-top, just as players want the series to be — or at least those stupid players who demanded answers and sent him death threats. After all, this is what we like, isn't it? Senseless, testosterone-fuelled action with ninjas and fart jokes? Kojima sure knows how to please a crowd! Even if it means ruining whatever he was trying to get across with Metal Gear Solid 2 in the process.
PART FIVE: Beauty & Beast Unit
