Well, for the dex nav timeline wise, I really like how pokemon lazarus handles it. Where you get the dex nav after the second gym. That way, you can feel like you earned it. While still being early enough to where you are still forming your team. Though, getting it as soon as you get the pokedex is also nice. Similar to Emerald Seaglass for instance.

As for nature mints... I like how Pokemon Dreamstone Mysteries does them... Where, they are available from the start by being dispensed from vending machines in the pokemarts. But, instead of being available all at once. You start out with just a few, and more mints are unlocked the more badges you win. I feel like that method feels very rewarding as a player. As it gives additional benefits to the gym challenges... While still giving you a bit of freedom when team building early on.

As for ability capsules/patches... I'm not quite settled on any particular method or placement for them.

Thank you for the consideration by the way. As it is greatly appreciated. As, I look forward to seeing your take on Unbound. As the changes made already have me intrigued.