This is becoming a transition show, which anyone should have seen coming. They want to do the origin story of the tos crew through strange new worlds. This is an inevitable tie in. Pikes story was always going to lead to Kirk and the tos crew.

So I guess there is no point in continuing Flash comics. I mean the the dude is literally unbeatable now. I mean what kind of jank bad guys are going to be better at stopping the Flash than Supes? Flash always wins because he is now too fast. End of story. End of comic. No need to print more.

If Neo truly was a part of the system of control, then it is entirely possible that he was the only One. When his ability was first discovered and made a part of the system, it would be childs play for machines that created humans from scratch to be able to clone Neo and reintroduce him into each version of the matrix. The same is true for Trinity. So in my opinion, yes, Neo very easily could have always been the One in every iteration of the matrix. Having the innate ability to change the matrix would not be something that just constantly keeps being created within entirely different humans. It would have been tied to his DNA and uniqueness.