Megaman and Megaman X are the same person. Dr.Light puts Megaman in the capsule after having given him the chip that allows robots to think and feel like human beings. Or did you forget the intro movie to Megaman X? Good gravy, I even remember some of the X-Hunters talking about "his archaic weapons." Several mavericks and even Sigma have referred to him as old, a relic even. He's probably the oldest robot in the X timeline.
Okay, now that you've said this I'm giving up on you. You clearly don't know what you are talking about or are an elaborate troll, I mean you even think OVER-1 is X and you have no idea what XOver even plays like with the Fire Emblem thing.
This already happened with Bioshock.
What happened? That they made a different game that still stuck to the Bioshock universe but had more emphasis on the action instead of the horror? It was probably far better that Infinite wasn't in Rapture a third time, it was already explored twice and didn't need to be rehashed again.
You want to talk about games that get the so called "CoD Elements" added in, Dead Rising 3 should be your target, not Bioshock.
I don't think there's anything left for me to say.