Ralts and Baltoy seem a bit strangely related, and might be resistant to each other, so hopefully you have a clear idea behind that. Other than that, those are Gen. III Pokémon, and as such making Arceus central to the plot may come across as anachronistic, and slightly out-of-place in such a context, so that you might want to use starters more closely related to Arceus, or use Arceus alongside the Gen. III legendaries, if you absolutely had to, but then you'd need a good reason to do so. From the post-game segment onwards, this just seems to be adding features far beyond and unrelated to most of the game that has actually been planned, and it might be worth emphasising the core game before adding most of these details and elaborations, so that you have something that you can elaborate on, in whichever manner from this path. It might also seem as if everything is selling something here, from the game 'selling,' so to speak, the Fly substitute, Pokémon Centres now also 'selling' things apparently related to them somehow, and so on, as opposed to the fairly specialised use of currency in the original versions of these games, before the ROM Hack. As they are now, the features increasingly come across as a few things that other games can do and this one will also do, rather than as things which relate organically to the rest of it, and they don't come across as part of an 'idea' so much as things that could or could not arise at some point in the idea, so if the game were just to be created as a decoy for a few features, you might wonder why. It's not clear if there's enough about this game that it already seems like an important part of the idea to include certain modes of complementing players' perhaps enthusiastic transport around it, a post-game, and so on, but in general it might make sense to explain the opposing team's aim, and the other things which would induct the player into the game, before figuring that part of the game's plot is that the player plays it for a long time, and past its actual content. Otherwise, I guess there's something of interest there, but it might require more coherence between its disparate fragments before it's more of a utile idea from whatever's there.
