If I was writing a Metal Gear Rising sequel, I'd do exactly the same thing Metal Gear Solid 2 did with MGS1, but with Metal Gear Rising 1 and MGS2 itself. The prologue-chapter has Raiden investigating "a new type of Metal Gear" ("We need to find out whether it's the kind that's equipped with nukes, or if it's like Excelsus and it's only called 'Metal Gear' as a marketing gimmick!"), he starts out equipped with just a blue sword that only does nonlethal damage, and it ends with him seemingly dying due to the baddies pulling an outside-context problem on him; after that, the protagonist is a new character, a woman with the codename "Vapor Snake" who's some new variety of cyborg ninja.
Like I'd be ridiculously obvious about how it's doing the MGS2 thing, there'd be all kinds of references, i.e. Vapor Snake's onboard AI assistant has an avatar which looks and sounds like Roy Campbell in Playstation 2 graphics and namedrops the "in part your own creation, cobbled together from expectations and experience" bit, and Snake replies with a comment about having "completed three hundred missions in VR" as the reason why she'd been thinking about Campbell. GW is back and positively identifies itself to Raiden by saying "Turn the game console off right now" and "I need scissors! 61!" One of the main NPCs would be the ghost of Monsoon possessing one of his spare cyborg-bodies in a way that references Liquid Ocelot; he refuses to "talk about memes" when prompted because everyone thinks he's referring to funny internet pictures instead of meme theory. The main villains set up Vapor Snake with a homoerotic nemesis in the form of a cyborg samurai a la Jetstream Sam. Nanomachines do even more ridiculous bullshit.
