I think a big part of the reason is just that you are not playing Solid Snake. You went from playing a total badass that has seen it all and has a cavalier attitude toward the world to a guy who is having relationship issues in the middle of a huge terrorist activity. If that isn't enough they are constantly reminding the player by showing Snaking doing what Snake does. It starts to become "Awww man...I could be him" and that is the big deal.

In a movie this would have played out just fine because Snake is perfect for the role in the story. Raiden would have been fine as well. You are a third party observer in a movie. In a game, to a certain extent, you are actively taking on the role of the character and come to embody that character. I don't care how interesting he is from a third person story perspective. I don't want to be this whiny little bitch w/ girlfriend issues. I just want to be a bad dude and save the president from ninjas!

That said, I still like Raiden but would much rather play as the gruff badass that is solid snake.