Yeah, I definitely enjoyed writing the battle between Diamond and Gallade vs his father Riley and Lucario. Probably the most memorable moment aside from the war on the snow route. Had I finished it, I don't know if there would have been a Pokemon League. I don't even think Diamond would have completed all of the Gyms because the focus was no longer on becoming the best Trainer, it was about saving the world. However, at some point Diamond would have succumbed to asking Dawn out lol.
What I usually do when I write is map out what I want to happen, volume by volume. I have a general understanding of what I want to ultimately happen when the fic ends, but doing it by volume is easier on my mind. Like right now, volume one is my focus, but I already know how the ending will probably be. Right now, I'm looking to get done with volume one before posting my fic and then working on volume two while posting one chapter a week.
I'm glad you got that feeling! The original Elite Academy was inspired by GX and a hint of Harry Potter, but I'm going to move away from that a bit. It's going to be hard to make an academy fic without taking ideas from those two, but I'm going to try my best.