No he simply said that it isn't a mainline game and it wasn't directed by him, the story is cannon, it's just not a very important game in his mind, which I totally disagree with, he fucked up the story and timeline beyond repair when he wanted to ignore PO during the development of PW and had to actually continue PO's story points without even telling you that it is, making the whole thing unnecessarily convoluted. To be fair, Peace Walker makes no sense without Portable Ops, and it outright contradicts the ending of Snake Eater if you leave PO out.
Because the appeal of The Patriots was the idea of them being in the shadows and completely anonymous, their mystique was going to disappear the moment they revealed their faces, no matter who they were. There's no win-win situation here. Most people didn't like the reveal that the Snake Eater cast was the Patriots, but it doesn't really make much sense to use anyone else. It's not like the Metal Gear universe is sprawling with characters.
Play MGS2 today after playing all the later ones and you can clearly see that the directly it set up has nothing to do with what MGS4 did later on. MGS2 was truely going to be the last one, they just fucked up the ending and made everyone want a continuation.
I always liked Raiden, you'd have to be very stupid not to see how bad ass he is in MGS2, where he does things not even Solid does, he shows a type of cold blood and comes across the typical "this guy looks harmless yet he'll fuck you up till next year" kind of appeal. And most people say he's whinny, yet I like that personality way more than Solid Snake's "yes boss, I kill everyone, no questions asked" attitude that Liquid Snake mentioned in the first game.
Raiden is constantly questioning his superiors and everyone else (sometimes outright just hanging up on the coronel), he doesn't hesitate to shoot first and ask questions later (ask Vamp about this, Raiden's way of saying "hi" is by pulling the trigger) and he's generally harder to deceive since he doesn't trust anyone.