>>40803037HMs stop being battle moves and stop taking up slots. Pokemon that qualify can be used to traverse the obstacle either as soon as you get them or with a gym badge, no further requirement.
Natures and IVs can be trained with certain regimens.
Go to the workout gym and plan your Pokemon's EV and IV growth, with their base stats shown as green bars and the EV+IV value a little blue bar showing how much it can change from the base. Every battle works towards decreasing or increasing EVs in a stat toward the *planned* value, so you can gradually change the distribution naturally over time while still playing regularly.
Repels replaced with repel tags that you can take out that keep away some kinds of Pokemon. Some even attract certain Pokemon. You never need to reuse or restock, you just have them.
Every route has a boss trainer. Maybe it's a bully. Maybe it's an ace trainer from far ahead. You don't actually have to fight them, and you NEVER have to watch a cutscene about them riding up on their shitty bike calling themselves a "heartbreaker"
Ledian's new ability makes its pitiful attacks damage the entire enemy team except any Sheninjas.