My biggest wish is that they'd stop with the 'one step forward, two steps backwards' mentality.
Comparing XY to BW/2 - the change from sprites to models was good, but the game had zero plot and close to 0 memorable characters; the overall mechanics are better (the exception being megas), but there's no postgame and almost no challenge.
Does anyone remember ramos? Flare scientists or even lysandre? While unova had its own share of forgettable characters (alder..), the games sidetracked and had you interact with characters. Unova also had the best evil team to date, while kalos...did it even have one?
The challenge, or lack of, is by far the biggest issue. Every game is less challenging than the one that came before it. Challenge mode was a good sign, but then came kalos.
I haven't followed SM news since late june, so I know not whether they showed any hints of fixing these problems, or if the new evil team is yet another rocket.
/rant
Some other things i'd like to see:
-Official nuzlocke support
-The return of chars from previous games like looker, zinnia, emma (the only interesting char from XY)
-Type changes for pokemon like the gummy line (water?) and floette line (grass?) among others
-More breedable legendaries. An idea me and a friend came up with was an ice/dark werewolf that would be able to breed an ice(/fairy)
white wolf with its own evo line (basically, a cursed wolf and its purified offspring)
-Atlantis-esque town, underwater. Perhaps the building in the center of the map could be the entrance to the underwater post-game area.