Currently Online 
First, I think there are a couple of directions another 3DS Pokemon could go in, especially thinking back on the differences between the DS games. My main desires are either for Sun/Moon to have a stronger story OR for the game's world to be more three dimensional.
First, by a better story, that could mean one of several things. There could be a more interesting plot through the game like there was in Black/White, a dynamic rival character like in Gen 2, an emphasis on a friendly character with their own character arc, a bunch of side characters and world building, or whatever. I kind of get what they were trying to due with Kalos (make a nice, pretty, and pleasant region where a villainous plot is almost pointless), but i'd like to see a strong story.
Thing is, this might get in the way of my other big wish, for what I call a "Fully 3D World."
You know Route 110 in Ruby/Sapphire? There's a normal route with grassy terrain, but you can take a short cut by surfing or use the cycling road overhead. You could take one route for wild Pokemon, or another for trainer battles. I REALLY would like to see that basic idea of multiple paths on the same route explored. You know how HM's are annoying? What if each route had a basic route that required nothing, but also alternate paths (not just items0 you could only reach using Cut or Surf? Or what if you explored an area multiple times, using new items and abilities each time? Making each route worth revisiting would be cool.
As for more simple things:
- 100+ new species. Kalos only had 70-odd new varieties, and even if we include Mega-Evolutions, it's been a somewhat small roster this gen. Hoenn had over 130 new species, Kanto and Unova over 150 each. And certain Types are somewhat underpopulated (Ice/Steel/Fairy/Dragon) and can use some non-Legendary members. Or even Legendaries.
- Buff Grass. Currently, Grass is among both the worst offensive and defensive types in the game. Seven types resist it and Grass has five weaknesses. And I appreciate their immunity to powder-based moves that cause status ailments, those were largely done by Grass types anyway. I didn't think I'd say this, but seeing how Gen 6 already messed with type advantages, I'd recommend taking away Grass's disadvantages to Dragon and Flying at least. Those two don't make that much sense anyway.
- Be willing to experiment with new and underused type combinations. Of the 171 type combinations possible, 38 have never been used and 60 are only used by a single line. I understand the use of monotyped Pokemon, but do wee need more Bug/Flying? Let's see some Poison/Flying mons that aren't Zubat! or non-Magnemite Electric/Steel! I would love more than Surskit to work with for Water/Bug.
- Make character customization more immediately available. It was good in Xy, but should have been available before reaching a barber.
- Make breeding easier by spelling out which egg groups Pokemon are a part of. I don't want to go to Bulbapedia that often.
- Develop the Pokedex. It's amazing how little good that thing is. Show the typing of Pokemon we've beaten but not captured, let us add info based on NPC gossip, provide lists of moves Pokemon learn as we unlock them, etc. For a supposed codex or encyclopedia, it feels more like a check list.
