I don't know anything about comic/novels but i will give it a shot regardless.
MGS2 Raiden would most likely not stand a chance against kusanagi, At that point he is a trained operative where even normal and trained soldiers could as-well be a threat to him. Even if he beat all those metal gear rays it's not the same as fighting motoko, She could very easily hand his backside on a silver platter if it comes down to a one on one CQC fight due to simply being overpowered in almost every way. In my opinion it is a mismatch.
Motoko outperforms him in experience strength speed and almost everything, As in MGS2 raiden has almost no field experience outside VR training and is flesh and bone, He could dump an entire magazine from his pistol on motoko and it would not even make a difference on how horribly one-sided it would be.
MGS4 raiden on the other hand is a more fair match. At that point he actually becomes a threat with a actual cyborg body, Which is proven to be pretty darn strong as he could cartwheel gekkos around on metal strings. Although in durability terms i believe motoko wins there. All it took to get him weakened was a few hits from vamp and to run his own blade through his abdomen. Which would most likely not phase motoko at all seen as her cyborg body has gone through punishment that would make MGS4 raiden die. Albeit the real threat here against Motoko is the high frequency blade, It would cut through her like a hot knife through butter. Although even with joints missing she can operate with no problem as she doesn't have any need for blood. While on the other hand raiden does and bleeding out is a very real danger for him.
In my opinion this is a pretty close one, If motoko keeps him at range and shoots at his joints she could possibly disable him with her pistol, Heck she could just shoot him in the head and it would be enough to put him down. But if raiden gets up close and personal with his high frequency blade it's going to get nasty if he gets a good and clean cut on her. I would say a possible tie although i am in favor of raiden on this one, He is agile and could take a few hits needed to get up and personal to dice her up. I could really say he just manhandles her as in MGR his old cyborg body could lift a damn metal gear ray and his high-frequency blade cut through meters of what i assume to be titanium-grade material on the ray. But i won't because MGS and MGR are different in their power scaling. Waaaay different.
It's a very close one, This one depends more on the scenario and situation and even luck as well as personal preference.
Metal gear rising raiden though... Well, Motoko has no chance to ever hope to scratch him or even come close to the colossal strength and durability his new body has. He can throw metal gear rays up and slice them in pieces like it's a average workout for him and that's with his old body. His new one could tank a punch from senator Armstrong that shattered a metal gear into pieces and got up after that in a fighting condition to whoop Armstrong thoroughly and walk away towards the sunrise happily ever after. It's a one sided slaughter in MGR logic. The only thing i can see damaging him is special high velocity rounds, Although we are talking standard gear. So she won't have them.
And just to clarify for other posts, No. She can't hack jack. As his brain is literally a brain, Nothing like a cyberbrain. Wouldnt she need to find a way to get plugged in with him which would be incredibly difficult and awkward ? Or am i confused. Also Raidens brain has nanomachines in it IIRC. But i dont recall her having feats of hacking nano tech of any kind.
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