An example:
Would it be open world? If so would it be a larger world or a smaller world?
Semi-linear (i.e. a few branching paths that still eventually lead to the same destination. Being able to do a few things out of order etc.)
Or fully linear (game forces you along a set path with plenty of side areas that have little to no effect on story progression. Usually with interesting main story dungeons.)

As for the actual dungeons, how'd you design them? Would you require HMs (or an equivalent?)

I personally would take the semi-linear approach. Most mandatory story dungeons would be simple progression-wise but often have side areas that are more complex and rewarding with a few of them having Metroidvania-esque exploration (gaining an ability or item that unlocks more early game areas.) The optional areas would mostly be more complex from compared to their mandatory counterparts.

>>58013057 (OP)
There wouldn't be HMs, rather you'd get to use your Pokémon in those ways without them.
Example: There's a tree blocking your path, you have a Scyther in your party, it can cut the tree.
You see a body of water that you'd like to cross, luckily you just caught a Wailmer.

I'd also have alternatives in scenarios where you don't have such a Pokémon, like a pair of shears to cut down a tree, super strength gloves to push boulders, a swimsuit to swim, diving gear to dive and a flying taxi service on speed dial for fast travel.

>>58013057 (OP)
after the first gym, the player would have the choice of three different story paths that they can do in any order, but they're stuck with the one they pick until they finish it.
there would be HMs, and each path would have an HM specific to it (rock smash, strength, or defog) but completing the first path, regardless of what you chose, will give you fly, and completing the second will give you surf.
each path has two gyms, meaning that after you've done them all there's one final gym and then the league.

Depends if we are doing turn based combat, or action. Turn based, maybe something like expedition 33 but with a bigger emphasis on responsive turn based, action/real time I'd have to think about it, but I would say something like being able to switch control from your character to the pokemon or one of the pokemon you have out.