Have you ever played Dark Souls? Do that.
There is a direction the game pushes you in, but you can choose to do things out of order, and it won't hurt the overall game.
There are, of course, certain blocks. You have to wait til the end to challenge the e4, of course, and also you'll want to deal with the main villains.
But other than that, give the player freedom.
That's not to say that we should ignore story, though. Just make it more subtle, perhaps. Give Pokémon dex entries that explain some of the region's lore. Make key items have a history. Sure, add some exposition when talking to people, and make it so that when you investigate the walls of an old temple make some things obvious. This isn't going to go over a kid's head, but we also don't want to make it boring for someone over the age of 6, y'know?
Now, as for difficulty: I'm thinking if we keep gyms that the badges can be used to base the next gym leader's team on, or something. Give each gym leader enough teams to warrant how many different ways the player can challenge them. If you have to beat a specific first gym before progressing then obviously they'll only need one team, but you see what I mean.
I think we should keep Trials and Totem Pokémon, though maybe rename them. But they would be optional mid-game and available again powered-up in the post-game. These would also be an excellent way for the player to earn Z-Crystals or maybe even Mega Stones. And, they serve as optional extra bosses. Sounds pretty good right?
As for the dex, as long as it's above 80, has less than 9 legendaries, and has at least 5 new regional forms, megas, and exclusive Z-moves, I couldn't care less. Flesh out the mechanics instead of adding new gimmicks as an attention-grabber for one gen.
Also, remove SOS battles and bring back dark grass from BW and have that be how one obtains hidden abilities this gen.
Base it in a country that is somewhat less talked about Chile and Argentina, or Mexico, for example.
Done.
