I just saw the gym leader team that you has planned (yes, i haven't seen them before, shame me) and to tell you about my opinion I think the gym order needs to be redone considering that there'll be no field effects. With field effects, you could adjust some lower-tier monotype team with to be more suited in their respective order. However, now that there'll be no field effect, the gym order need to be chosen carefully so that each newer gym should have more difficult than the previous one. Of course that's not a must and it's up to you, as long as the gym order match well with the role of the leader in the plot. The team also hasn't been tested, I guess?
Anyway, I still think that this game has a lot of potential like, why don't we skip the academy part of the game? There could be filled with various quest and mission to finish the academy but I guess for the start just focus with your current plan.
Oh and just another suggestion, since we already know some of the backstory, the enemy's motives, etc. I hope that they don't decrease 'that surprise feel' when we finally play the game. So just be careful of spoiling the game's content too much. That's just my personal taste though since one thing I like from Reborn, Rejuvenation, and Desolation is that we don't know fully the exact motives of the enemy at the first place.
And for the technical part, since this game will most likely utilize custom tileset what kind of graphics you're looking for, 3rd gen, 4th gen, or even custom? Will you release the game in episodically or as a full whole game? Besides the concept and worldbuilding aspect, what progress is being a priority now? Sorry for so many question, I'm just overhyped.