MGS2 has one of the most impressive stories in video games and manipulates the feelings of the player to an insane degree. And there is always a laugh I get at people hating on Raiden for not being Snake, because that is EXACTLY the reaction it is trying to get out of you. Seriously, play through the whole game again and start comparing how much Raiden is trying to be Snake, in a mirror of the player trying to be Snake. He knows what he is doing, he has so much virtual training!
Also, next time you think Raiden is being "whiny" actually pay attention. He is right about the mission being all wrong. Every time he brings up an objection "Campbell" tells him to get back on task and complete the mission and stop thinking.
MGS2 is layers and layers of ideas and every character has different motives and the manipulations involved and the concepts and depth are actually much much smarter than every other MG game.
Well, let me explain it in another way. I do understand what Kojima and his team were aiming with the story, trying to mess up with the players and their minds, by blurring the line betwen what was real and what was not, (this of course, in terms of the game reality). I also understand that Raiden has the rol of being the new Solid Snake, mirroring the the gamer trying the same.
But all of this don't work with me. I still find it stupid.
When I think MGS I think Solid Snake, not Raiden, that's the reason I hate Raiden, for not allowing me to play as Solid Snake for the mayor part of the game. It's like playing a Legend of zelda game where you can't play as Link, but another character trying to be Link, Metroid without Samus, Tomb Raider without Lara Croft, etc. That's the main reason.
Strangely, I find Raiden an interesting character in various aspects, but the main problem is still there for me.
In the end is just a matter of tastes, and I won't try to convince you to think like me. Like I said, MGS2 is a good game, but those aspects make me love-hate it.