Snake is sort of a deconstruction of the legendary war hero, whereas I agree that Raiden is a deconstruction of the player. I never really was bothered by Raiden getting picked on in the game except with Rosemary who I felt undermined his character and the game, the rest of the stuff is just the series quirky humor but listening to Rosemary go on and on easily pulled me out of the experience and was just the first of many obvious clues that something about the mission wasn't right.
I don't necessarily hate the post-MGS3 titles, MGS4 does just as many things right as I felt it did wrong and I forgive it more than I should cause I understand that it was trying to get the series out of the corner that MGS2 kind of wrote it into, but I also understand that it was Kojima's intentions to leave MGS2 as it was. I don't think it was an accident MGS3 was a sequel that barely connected to the events of MGS2. Kojima gave in and gave the fans a sequel but not the one they asked for.
Portable OPs is pretty forgettable and I'm waiting for Kojima to finally say it is non-canon but Peace Walker was actually a pretty decent story by the end even if I felt it simply retreaded on character development Big Boss already received and transformed The Boss into some mythical Saint figure. Hell, while I can't justify buying Ground Zeroes cause it feels like a rip-off I can say that what I've read about the story has me a bit more excited about Phantom Pain.
I'm sadly the opposite of you, I play MGS2 more for the gameplay than the story as I can't really get behind the plot of this one.
To leave this on a positive note, these are hilarious and must be viewed: