Literally everything except for the catching mechanics, honestly. PLA was a great game made extremely badly, with far too many unnecessary systems that only served to weigh down and outright hinder the enjoyment that could be gained from exploration and catching Pokemon.
To name a few things:
- Crafting was unbalanced and counter-productive for anything that wasn't a basic level Pokeball, and needed to be designed properly so that resource gathering was more efficient - I do NOT want to watch the same animation over and over, thank you - and worthwhile.
- Fall damage just needs to be outright removed because that has no practical purpose or place in the game other than to annoy.
- There needs to be some kind of metric put into the game so you won't be chased by a level 4 Shinx or Bidoof across half the map when you're packing a team of Pokemon in their late 80s. It's fine to start with, but progression is a thing that needs to be acknowledged.
- Battles and levels need to be re-balanced so that they're not utterly random and unfairly stacked against the player. Sure, if you get into a battle against a horde in the wild, that's your mess to sort out, but having trainers use two Pokemon at a time and limiting you to one? That's just bad design. Levels also need to have more meaning than just the moves you can use.
- Please, for the love of Arceus, hire people who know how to build a game properly so it doesn't run like crap and look even worse. I don't really care about visuals and framerates and all the rest but I at least want something functional.
- Hiring someone who can write a story would be a good idea too. It also shouldn't be entirely placed in the postgame, forcing you to play through the entire game before getting any narrative context. This isn't bloody Monster Hunter.
- Sidequest variety, for crying out loud. This is a problem with a lot of JRPGs, but at the same time, I'd call them out for having a bunch of meaningless filler crap in them too. More quests that enhance the narrative and worldbuilding - like the quests in Xenoblade, basically - would be better than just "go and find 108 spirits that we're not going to mark on the map" and "go and fetch me this Pokemon" etc. Put some thought into it.
- More to do on the map. This could tie in with the sidequest variety, but the only difference between PLA's areas and SnS' wild area was that PLA didn't have the obnoxious glowing red pillars that signaled raid battles and had a few different modes of traversal. It was still a bunch of empty space with a few Pokemon scattered about. Travel time is not playing the game, it's a glorified walking simulator. Condense it down, or fill it out. Don't just make space and leave it at that, we moved past (or should have most past) the empty open world design with Shadow of the Colossus.