You know how sometimes the Pokemon gym has a puzzle inside it? Just make a Pokemon gym look like a 2D stigma and have the gym leader named squally XD
I actually spent a couple years working on a romhack of Ruby. New region, story, characters, everything. Still have the files on a drive somewhere. Sad part is the hack got sidelined because I was deadset on having about 100 new Fakemon for the region, and I was bad at designing new Pokemon. The maps seemed to be really well-received when I shared them on other sites, though. Edit: I dug through some old posts and found a gallery of what I had so far.
Make all the gyms based around the finest maps on Forgehub, with the gym leaders being the map authors. If co-authors, then make it a double battle gym. "Pokemon Forgehub".
Follow Pokemon Conquest. NON-MODERN day pokemon. switch pokemon centers with taverns where you sleep. Equip-ables (like the lucario staff) to store your pokemon. Would mix things up. Rival from hometown joins evil organization. (possible friend and trying to get them to quit them). If non-modern maybe like crusaders? People who think they're holy. Seasons matter. Seasons has been added to pokemon but it hasn't really changed much. I'd like to see something like the animal crossing system where you can only catch pokemon during certain seasons. Pokemon follow you and maybe you're also a pokemon? gear and weapon equipables? I don't know what's possible with this editor. Do 'Gyms' in any order. Lastly, if there are any 'new' pokemon. Starters, but each one has 2 or 3 evolvements. This makes them super personal and special.
When I say that I mean different paths. for example gloom can evolve with a sun stone or a grass stone.