I'm sure it's already been said, but it sucks that certain pokemon can't be in certain balls simply b/c the balls weren't unavailable in those games (ie. Pokemon not available in HGSS can't be in an apricorn ball). And along those lines, I wish all the event exclusive pokemon would hand you an item that would trigger an event to catch in-game instead of just handing you the pokemon (ie. Eon Ticket). Not only would it be faster to get the nature and stats you want, it would allow them to be in a different pokeball besides a cherish ball. I hope these pokeball limitations are rectified in Gen 7 b/c it would be great to have a Keldeo in a lure ball or Diancie in love ball, etc.
Yeah, it only they would introduce some kind of Poke Ball shop, a shop thought would not only sell all the variety of Poke Balls you'd normally have to region hop to get but also sold Poke Balls you couldn't get like the Apricorn Balls and maybe the Safari Balls... seriously the Poke Ball shop in Lumiose City was not only a waste of space and concept (so I could buy a Premier Ball normally from it, woo~) but also a tease as they had some of the Apricorn Pokeballs on display!
Or heck, why not just start spreading the Apricorn trees all around the Pokemon World. I don't see why not, like I get you not including them for Gen III since they weren't compatible with Gen II games and you wanted to focus on the New Pokeballs. Fine. But when you brought them back in the Johto remakes I don't see why you didn't keep them around.
Actually looking through something I have a new annoyance: them removing fun key item. We all know GF just loves throwing away old stuff even though players liked them for new stuff for players to also like until they get rid of them too. Here's a quick list of some notable ones:
Coin Case: RIP Game Corner.
Poke Flute/Colored Flutes: Those were fun bonus items to have. Sure they made some medicine obsolete but I felt that was because your were expanding your capability and savviness as a trainer (heck, most become obsolete once you can guy Full Heals). Plus curing Confusion & Infatuation without needing to switch or using a once use item is handy.
Soot Sack: While maybe not always soot, I liked the idea of having an item which collected something as you're just going around. Like I always thought they should maybe have a Soot Sack for garbage cans. You know, give those garbage cans you always see around yet have nothing when you look into them? How about a "Recycle Sack" which stores items you find in trashcans you can then bring to someone to turn into items.
Fame Checker: Learning more about the characters within the game and maybe adding some depth to them that our brief encounter with them in the story wouldn't normally be able to show? YES PLEASE!
Teachy TV/Journal: While not essential, it would be nice to have an item you can look up basic tutorials in. If you want some more use with it you could maybe even have it include a Type Chart.
Vs. Seeker: While the AreaNav was nice, I'd also like to have an item they could force trainers to immediately battle again instead of having to run around between routes until they felt like it.
Gen IV's Bike: Acro and Mach Bike is nice, but having both of them in one bike is even better (and you don't have to waste a quick select spot on a second bike).
Seal Case: Yet another chance to add customization. Sure Pokeballs all have their own release animation, but Seals add many more options. Plus you could maybe even have a combo thing where the Seals animation will change depending on the Poke Ball used with. You could maybe even have that play a factor in Pokemon Contests.
Explorer Kit: More of seque to the Sinnoh Underground, it was a fun concept and I think they could have recycled the idea. It also didn't always be an underground place.
Poketch: I liked all the little apps they came up with it, wished they kept them for the other future Trainer Tools.
Berry Pots: A great idea for those who don't want to keep running back or remembering where they planted Berries. Also I could maybe also having Apricorn Pots.
GB Sounds: Mainly restricted to the remakes. Why was there no GBA Sounds in ORAS?
Roller Skates: I hope they keep them, though maybe letting us choose when to put them on.
Eon Flute: I want them to keep this but I don't see how unless they shove the Eon Duo in every game. Maybe instead of this item specifically they should just make Soaring a mechanic a specific batch of Pokemon could do.
Scuba Gear: Would also like if they kept diving in the game. And it doesn't have to be as expansive as Hoenn's. Maybe have certain diving spots that show off different kind of water biomes.
PokeNav Plus: Or at least moves its features to other places. Like you can have the DexNav just be part of the Pokedex and the AreaNav just be part of the Town Map.