I think you mentioned in a previous chapter commentary that Chaletwo jumping forward in time to only be visible a few minutes every year isn't going to work, considering it is established (in this chapter) that he would be leaving the time he's "anchored" to, and as the War approaches he should get pulled back to the right time. If we follow on the idea that Chaletwo consistently jumps forward in time to appear for a few minutes, the way I would envision this happening is that as he gets further and further in the future toward the War, he gets his power drained ("prematurely" because he's only "existed" for 5000 minutes or whatever, I would think), and then eventually bounces back to 5000 minutes after his creation. This is how I see it as working - feel free to correct me if you have a different version! But if I assume this is accurate then my question is, so is Chaletwo just incredibly weak for the remainder of his existence until he "catches up" with the War later on? I know this is all moot because that's not going to be how Chaletwo operates in the next revision but it is something I thought of recently that I was curious about.
If Chaletwo did this, then his power would be drained as if he never time-traveled at all, through the anchor. He'd still be at the power level he would be at after 5000 minutes in his own time. He wouldn't bounce back until he's lived the full nearly 1000 years.
1) without Mewtwo-guy changing your idea for what happens to Mewtwo and affecting everything else, do you have any idea of where the story might have gone after that?
This either happened after or probably had no influence on the Mitch-is-Chalenor reveal, so that would probably still have happened. I'm also pretty sure I'd been planning the ending with Mewtwo^2 being out long prior to this. So, as things were headed at that stage, we'd probably have had an ending where they just fight and take down Mewtwo^2 (well, I might still have ended up with Mark helping him resist, don't think that'd have been related), and Mitch joins them and turns out to be possessed by the ghost of Chalenor. But that'd just kind of be it. The Destroyer would be random giant pterodactyl or something. Nothing of note would have happened before the last War, and Mew's words would have been truthful.
2) you mentioned the mechanics of how Pokeballs and soul gems work regarding the War, but when it came to how it would work now that Chalenor's dead you said what you thought Mew would think, but not what you would think would happen. Any ideas on that front?
I said that maybe it would have, and that's what I'm inclined towards - Arceus's design actually being flawed is part of the point here, and if there was a real possibility of everyone escaping the War under these circumstances, I think that has a nice punch to it, both because of that and because of Mew's fierce motivated denial of the possibility. But, you know, if for some reason I later came up with something better, I'd do that.