>>45008557>you can challenge gym 1-3 in any order, but you have to do them all before gym 4-6That could work! It would preserve progression without totally locking you down.
Alternatively I'd like to see an approach like Hollow Knight where you have multiple ways to get places so for the most part the more you explore or already know about the areas/mechanics the more open the game becomes. Sure you'd have your early areas with only a few paths but once you've figured out the basics you can go where you want. Find a water pokemon and hunt down surf early to explore the ocean, find an island and challenge a gym there, or see some dive spots with ruins below you to encourage you to find that hm and when you do get in there you find a sealed off cave entrance you could clear with strength or rock smash to open a tunnel leading to another set of ruins far away you might not have found until later or you could have gone there first and found the tunnel to the underwater ruins, or you could come across a land mass that's all cliff faces that at first glance may only be accessible with rock climb but search around and you can see trickles from a river that's dammed up where you can open up a waterfall by solving a puzzle to knock away the blockage. You could get fly asap and go anywhere but it's tricky to land and if you haven't been there before you've got to get it just right otherwise your pokemon would get scared and pull back up after only getting close enough to see some land marks and potentially an alternate access point so flying isn't a waste of time but also doesn't devalue the other transportation methods. Gyms scale like those template threads where what team they have and level they're at depends on how many badges the challenger already has, trainer levels are a mix of scaling and predetermined so you don't get veterans with level 10 teams or new kids with teams in the 70s but most are around your level +- a challenge factor.