I think the majority of the backlash on Raiden was because people wanted to play as Snake for the whole of MGS2. At the outset, he appears to be the exact opposite of Snake, a green nancy boy, unsure of himself, pussy whipped by his girlfriend. But of course as you learn more about his past over the course of the game he becomes much cooler and interesting, but I guess a lot of people already decided they hated him before that point.
I just know Kojima is pulling a total "fuck you" to the Raiden haters by making him a total badass that you
WISH you could play, but he'll never give you the chance. (Until MGS4 Integral/Substance/Subsistance/whatever

)