I like the idea of tournaments and quests/missions. Especially if missions take place as part of a larger plot.
Hmmmm.... as I said I'm not sure I want to GM (and who knows, OP could pop in and then I'd feel bad) but if I did I'm thinking of ways to combine the storyline of a game I've made before (
Take a look if ya want but don't judge me >_<) . I'm thinking a possible origin story for the crime syndicate in that game (Team Fusion). Perhaps, unbeknownst to the population, the young, beautiful, and mysterious headmaster is the original "prophet " of this organization. He's got a few disciples among the teachers at Celedon University and while the schools mission continues to be mass producing kick-a trainers, a new interest in the arts of Fusion begins to take over. The game would primarily take place below the level of these forces but as things progressed students may end up having to pick sides. Idk that I'd present either side as "the good" or "the bad" just different views on the world and its end. Mwahaha.
For the school itseslf, if it were me I'd write it along the same 7yr span as the HP books. No one would probably be playing first or second years so maybe we'd just leave them off the table for main characters. Perhaps students start out as just generalized trainers but are expected to specialize somewhat as their careers go on. For example, by the end of their third year students are expected to "pledge" to a house (water, fire, electric, or grass) which would lock them into a style or team (though I don't think it should lock them into a type so much that just seems a bit rigid). Each "Team" would have a sort of personality. I'm thinking:
Fire - Focus is on battling. Hot headed. Focus on Valor (tehe). Similar to Gryffindors in archtype but not always good guys. Perhaps their "territory" is some sort of school dojo or battle arena.
Water - Also focused on battling but also being smarties. Idk I don't want to be too rigid on the personalities but these are our Ravenclaws. Perhaps more inclined to fusion but who knows. Cool and collected. Territory is the pool.
Electric - Hardworking. Fun loving. Easy going. The Hufflepuffs but still pretty cool. I imagine their territory would be somewhere fun. Maybe a small amusement park in town.
Grass - A paradoxical group I think. Very smart but also ambitious. Not perfectly analogous to Slytherins but I've got a possible baddie I'd like to put in this group. Science geeks. Most Pokemon Proffesors were in this house. Territory is a park surrounding the Celedon gym.
Aw heck lets just be lazy and align them to Go! teams. XP So you've got Mystic House, Valor House, Instinct House, and ehhhhh hm... I'll think on the last one. "Tournaments" could happen between houses on a monthly basis, plus a couple of tournaments with trainers outside the academy, and a big "end of the year" tournament. A student who wins this tournament ends up with essentially the same rank as a master.... which makes for good rivalry as each house wants to have the champion.... Realistically I've never been sure how to run good tournaments in post by post games.
Before pledging to a group students are just categorized as "normal" type. They've got a territory of sorts but it's the student community center plus a coffee house at the base of a clock tower. Additionally, the clock tower hosts the "Student Council" a collection of talented students who were either voted in or hand picked by the headmaster meet (cause I feel like every school-based anime has a student council). They also get to go on smancy quests sometimes that connect to the larger plot. Perhaps our varied characters are all on or friends with someone on the council and thats why they get to do cool things.
I really don't want to hijjack this because I feel like there are a lot of people here who would be more dedicated to it than me and like I said I'm busy in rl but let me know if this seems like an appealing start because I could start mocking up something and then if the OP comes back (or someone else comes up with something) I'll just put it on a shelf for later.