I agree with the last paragraph. MGS4 Raiden was a "You WILL learn to love him!" thing.
They tried to make him the new Grey Fox. Everyone loves Grey Fox because well... Hes cool. Hes a cyborg ninja that makes Otacon piss his pants. He saves you from REX and was even in the original 2 Metal Gear games where once again hes a pretty cool guy. Didnt he also make an appearence in Portable Ops?
On top of this, Kojima once even said he wanted to make a game focused on Grey Fox.
In MGS2 "he" comes back for a short while. In MGS2: Substance you can dress Raiden as Grey Fox. In Rising you can dress him as Grey Fox.
I think Kojima realised he killed off a really popular, unique (at the time) character. He screwed up and Raiden was his way of "fixing" that.
