I'd be happy if they gave more pockets in the bag to sort everything in, as there are certainly WAY too many items just crammed into the main items pocket. If having too many pockets visible is the problem, then stick a few as separate inventories accessible in the Key Items pocket like what FR/LG did with Berries and TMs & HMs. Give Poke Balls their own separate pocket again. Maybe do the same with fossils and battle items. Heck, give us more free space pockets so we have the option to further organize our bags if we so choose.
Late reply, but I think you made some good points and I wanted to post my thoughts on them.
I agree that the bag needs an overhaul. If they can't have too many separate pockets, at least make the sorting function useful again. It was perfect in Gen 5 and then they had to screw it up so hard in Gen 6. They haven't even fixed it now, three game releases later. Even if you sort things by type, it is just a big mess, finding the right item can take far longer than it should. Having a better scrolling option would be great too. Once more, that is something Gen 5 did perfect which Gen 6/7 failed at.
Regarding the Mega Stones, they need to be better ordered as well. I understand that they are in Japanese alphabetical order (this was stated earlier, either in this thread or somewhere else), but why are they in Japanese order when you are playing the English version of the game? Feels like they missed this during the translation. It was okay in X/Y and OR/AS, but it should have been fixed by now.
While we're at it, I'm going to post some other things that annoy me in Pokemon.
First of all, regarding the recent discussion about Game Freak revealing too many of the new Pokemon for S/M. I agree. It made things a lot less interesting when I played through the games since I had already seen a vast majority of the new Pokemon, Alola forms and features before the release. I like being surprised by new things when playing through a new game, but that was not the case for S/M. I feel that they revealed too much for X/Y, OR/AS and US/UM too. If this pattern continues, they will probably reveal almost everything for LGP/LGE as well. Though it doesn't matter much for me since I'm not getting these games. I'm more worried that it will continue with Gen 8 though. And yes, I know that it's my own fault for looking at all of the things that they reveal before the games are released. That's why I won't look into as much from the pre-release material for Gen 8 in order to not spoil myself too much for these games. But it won't be easy. The reasons being that I spend a lot of time on Pokemon sites, this fandom isn't very good at handling spoilers, and Game Freak will probably reveal 90% of the games once more.
Onto something else. The Rotom Dex doesn't get enough hate. In S/M, when it was talking and you interacted with a NPC or did something else that darkened the touch screen, it would stop talking after a while. But this changed in US/UM. It
doesn't ever stop talking when the touch screen is darkened. Combine this with how it sometimes starts talking when the touch screen always is darkened, like in the Battle Tree or during minor cutscenes in the main story. This means that it can start talking in situations where it will never stop, unless you quit what you are currently doing. Sometimes I wonder if the Rotom Dex is just glitched or if they actually programmed it this badly on purpose. I don't know which, and neither answer is good.
I said before that I don't like the SOS mechanics. I guess the main annoyance I have with them is that they are just a big waste of time. If the Pokemon calls for a partner and doesn't succeed, that still wastes a few seconds of play time. Combine this with all the times they call for a partner when you don't want them to, and the sum will be several wasted minutes if you play the games for long times. I really hope they get rid of the SOS mechanics (and the Rotom Dex too for that matter) in Gen 8. If not, I don't know what I'll do.
I have seen some people complain about the fact that it is not possible to skip cutscenes in the games. While I don't mind the story cutscenes myself, I agree that it should be possible to skip them. I would actually like them to take it one step further. I want minor cutscenes to be skippable as well. Things like when a Pokemon evolves, when an egg hatches, or when you use Fly/Charizard (especially to Poke Pelago, that's the most unnecessary thing ever). It just gets boring to see them hundreds to thousands of times. I have seen Pokemon hatching from eggs thousands of times throughout the years, right now I just want to skip the hatching animation so I can go directly to the status screen and see if it is what I wanted or if I need to continue breeding.
Of course, this should be optional so that those who want to see these animations still have the ability to do so. I can imagine shiny hunters wanting to have them on, to add another element of tension and surprise when breeding for shinies. Overall, I feel that there are several things in the Pokemon games that would be better if they were optional instead of mandatory. That way, the games could be customized to suit every player's personal choices in terms of playstyle.
On to something different. Pokemon sizes in the 3D games. Or rather Gen 7. Some Pokemon like Wailord are much smaller than they should be (realistically). Yet they had no problem making Alolan Exeggutor so tall that it barely fits on the screen. In reality, it should be smaller than Wailord which is taller than it. I haven't had a problem with Pokemon sizes before, but I do now. I haven't had a chance to compare Alolan Exeggutor to Pokemon like Mega Rayquaza or Mega Steelix which are about the same size as it, but if I were to guess, they aren't as tall as Alolan Exeggutor.
Next up, something I like. Professor Kukui has a secret identity. He's the Masked Royal. This is actually quite a cool thing. So why am I saying this here? Because this is handled
terribly in the games. They literally tell you right away that the Masked Royal is Professor Kukui. I was so disappointed when I saw that. As someone who doesn't always figure out things like that, I would have preferred if they had actually kept it a secret for a bit longer or for the entire game, making it more of a mystery. Professor Kukui has a cool secret, but the execution of it in the games is just plain awful.
A very minor thing, but I find it annoying that the sound effects when you win prizes at the lotteries in Festival Plaza are the sound effects that were used when getting your Pokedex evaluated in previous generations. It just sounds so out-of-place to me and I find it annoying that they had to use just those sound effects there. They could have used different ones instead.
Something I just learned recently is that when you are riding on a Pokemon through Poke Ride, it gives you a lower chance of encountering wild Pokemon. This isn't that much of a problem for Stoutland, Mudsdale and Tauros, but it is for Lapras and Sharpedo. Why? Because in order to encounter any Pokemon while surfing, you have to use the Poke Rides to start with. This is annoying when you are looking for a specific Pokemon while surfing. I remember that it took me a long while between encounters when I was looking for Lapras in Ultra Moon, this must have been the reason. I really like the Poke Ride system on the whole, but this part of it feels flawed.
There are some Abilities that I find a bit annoying. Or rather, I am annoyed by how some Abilities are handled in the games. The most notable being Minior and Shields Down. No matter how much HP Minior has, it is always sent out in Core Form. Thus, if it has more than 50% HP, it will be sent out in Core Form but immediately change to Meteor Form. In every single battle. That is just completely unnecessary. It should be sent out in Meteor Form if it has above 50% HP and in Core Form if it is below 50% HP. It is a very minor annoyance and I have gotten used to it by now, but still. I guess Wishiwashi is in a similar situation with Schooling, but it does make more sense to me since Wishiwashi has to gather its school (or so I imagine) before it can change form.