I guess you have a point with the VR business, though the cyborg ninjas and the mechas is also kind of shared across a lot of anime which is not necessarily cyberpunk. It's hard to draw the distinction, though I guess the litmus test is that MGS doesn't take place in a future dystopia. If cyberpunk explores what the future might be, and thus is implicitly optimistic about the present, MGS implies this is all happening now, and is more cynical about the present.