Open world. Progress into new areas is checked by battles instead of items/story eg Pokemon ranger tells you the area up ahead is too dangerous for a trainer like you, but you can challenge them and if you win they admit they underestimated you and let you pass. Other options could include bribing, having prestige as a contest winner (coincidentally the person on the gate is "a big fan" and lets you through for an autograph), or you're known for being a local Pokemon scientist (large number of seen/caught Pokemon).
All gym battles take place at a fixed level (your Pokemons' stats are adjusted accordingly) to force you to use strategy instead of sweeping them every time. Badges will let you progress by default (ie you skip the challenge to pass into that area) and grant you the usual "traded Pokemon obey you", but are only really necessary to challenge the league.
The trainers on the routes change each day. Some of them move about similar to how the legendary beasts do, others sort of "vanish" and are replaced by entirely new ones, but they may show up elsewhere later (drawn from a pool). More variety in NPC strength, with the relatively stronger trainers refusing to battle you unless you insist ("you wouldn't stand a chance"). Average NPC strength increases as the player advances but there are always some weaker trainers around for training.
Minimalist story. Things are happening in the world but you aren't forced to be a part of them. If you want to just do the gyms and league, you can do that without taking care of the local legendaries (which will just be unusually powerful creatures, not gods of anything) or the baddies, or teaching your rival the meaning of friendship or any other such nonsense. The player can make their own story up out of the events they chose to take part in. And no fucking cutscenes. Worst case scenario you get a few boxes of dialogue and maybe moved around a little. But it's not going to happen very often or take very long at all.
