There is a lot of stuff they could improve:
"Spinda effect" eggs: all eggs have a random pattern of spots and colors. Almost no egg is the same.
Return of HM dive: Also, randomized dive areas with a fossile to be found there and rare pokemon. Also underwater caves like the Team Aqua cave, just as a natural cave where many secrets can be uncovered.
Just new pokemon in the regional dex: Rather make old pkmn available once you get nat. Dex.
Legendaries: only new legendaries available. Dont care about how many. Many legendaries: more choices for battle, which is a good thing. If you dont like legendaries, just Think of em' as normal pokemon with a cool ability, much like Wonderguard. Nothing force you to use them...
More trainer outfits: much like the Team rocket suit or pokeathlethon suit in SS/HG. So you could choose the outfit you like the most.
Less hm's: lets just remove Rock Smash, waterfall and Defog... Strength can be used for Puzzles, so thats just cool
Season changes: Some places in Isshu should change depending on season. Like, if its autumn, there would be more rain and some places water would rise so you could reach other places. If there where summer, the water would sink, sou you could find a hidden cave or something. Also, some pkmn that could only be found in the different seasons.
Much more sidequests: many quests that would reward you with rare pkmn if you complete them. This should be how you could Get the master ball (Sidequest right before legendaries appear) also, let Team ??? Keep doing their stuff after E4 is beaten, and you will have to beat them when you're Champion as well.
New box system: make it possible to quickly change your pkmn, and a sorting system.
New, bigger battlefrontier: I dunno what should be added in it, just make it.
More backstory to the legendaries: Face it, there will be tons of legendaries... Just give them more story.
A new 1HKO move: Yeah, it would be cool with a new one. Fire, electric or Dark maybe? Just because they would look badass.
Bug legendary: yes, you know that this gen will bring you one..
Fossil legendendary: one, big fossil, with pieces of it shattered around Isshu.
New weather: thunderstorm?
Very cool ideas, I would be happy if all of those were put to use.
They definitely have to expand the box, I usually organize my pokemon by number, from Bulbasaur and Arceus and add alt form at the end (Unown, Wormadam, Gastrodon) That leaves exactly 12 empty spaces.
Nothing with Seasons please. I dont want to have to wait until winter for a pokemon when i get the game in spring