It fits better being post-MGS4, because there is absolutely nowhere left for the series to go from there, so you might as well go totally ridiculous "cyborgs have taken over the world and it is up to the one good-guy-turned-psychopath cyborg to save the world" or whatever Rising's story is supposed to be. It's all downhill from here! When things like this happen, it's usually time to contemplate starting over from scratch. Does anyone still want to see a MGS5 continuing the existing plotline?
I do think working it between MGS2-MGS4 made sense, though, because there's that gap that exists where Raiden goes from normal person to almost entirely mechanical, and seeing that transformation occur in-game would have been interesting. He was also supposed to be the one who found Sunny, so it would tie nicely into MGS4's story. All of the original concepts and ideas were great, in my opinion, and that was what made Rising exciting. Everything since has been a pretty big downgrade for me.
--
"When I was a young man, I had liberty, but I did not see it. I had time, but I did not know it."