All righty. I stayed up for...maybe 12 hours and read everything. Most of your plot twists I caught onto rather quickly but they were still well done, and several escaped my grasps completely.
But...I got tired of it.
A plot built on plot twists is tangled, deep, and well thought out. But I stopped caring about the characters, the setting, and even the Nuzlocke challenge itself, in favour of the plot. You could have had the most annoying protagonist and broken every rule in the Nuzlocke and I still wouldn't have cared, I would have kept reading for the plot.
But is that a good thing?
Obviously, to an extent, it is. This was still by far an amazing plot and there are MANY others who completely agree with me. This is a famous series on this site and the depth of your plot honestly made me a bit envious of what I plan on coming up with for my own upcoming storylocke.
So, you tried several new things, several old things, and created something brilliant. An excellent plot and story that can span time and space.
Ultimately, what I want to say is this: I hope you build from this. I hope you can, somehow, create a story that has all of this as well as characters I care about. Characters that MAKE me care about them. That always was the big thing behind Nuzlockes, as well as trying to spin the story as many different ways as possible.
I hope I didn't sound too harsh. Remember I stayed up literally half a day, that means no sleep, just reading this. I was obviously hooked and deeply enjoyed the run...but I'm a reader, a writer, and a reviewer.
We always want more from ourselves, and our colleagues.