What I think they will do next is a R/S Remake followed closely by the announcement of Gen-VI, with some Gen VI pokemon reveals.
What I want to see:
~ 3D version for the PC (long shot) or Wii/Wii-U:
NOT a game like colosseum or stadium. An actual adventure RPG game like the Gameboy/DS titles.
~An Eeveelution that can FLY dammit:
Wanted to do an all Eevee team for a while but the lack of flying capability puts me off, switching one out to fly everywhere irritates me, as does excessive walking. But Eeveelutions for every type would be awesome.
~Less "new" species of Pokemon:
We have enough as is! If I'm honest, I dislike the design of about 90% of the Gen-V Pokemon. Less legendary pokemon too! there's more and more each gen, eventually there'll be a game that is nothing BUT legendaries. instead.....................
~Expand on existing Pokemon:
Give some older Pokemon new evolutions. I always wanted Pinsir to evolve. Scyther got a bug/steel evolution when steel and dark were introduced. Pinsir should have gotten a bug/dark one to follow suit.
Other Pokemon that perhaps could evolve:
Torkoal, Dunsparce, Shuckle, Jynx, Pinsir, Delibird..........and so on.......
Just as long as they don't end up looking ugly or stupid, yes I'm looking at you Magnezone/Probopass!
~A new story:
Something a bit different from the typical - 8 gyms + rival + elite 4 + crappy bad guy team. Maybe even having the 8 badges beginning after your pokemon are lvl50+, like in HG/SS where after you defeat Lance you go on to collect the extra 8 badges. But instead of facing the elite 4, have it defeating the leader of "Team [insert name]"
"Wow I cannot believe you defeated "X"! now that you are so experienced as a trainer you should take the "Y" region gym challenge. The gym leaders of the "Y" region are unlike any other, they are very skilled and powerful trainers. Once you defeat all 8 of them them and collect their badges you will really be able to test your skill against our "Y" region's very own Elite 4!"
~More diverse trainers/battles:
-It's always bothered me seeing trainers will dodgy teams. A fisherman carrying a whole team of Magikarp, or a Bug Catcher with a team of weedles/caterpies. There's 649 pokemon now, why do they have a team of the same thing?
-Stop the bad guys using the same Pokemon/type all the time, Team Rocket pretty much all had Rattata, Zubat, Koffing, Ekans. For a group that steals Pokemon they sure do steal crap.
-Gym Leaders, The Elite 4, and top bad guys should all have 6 Pokemon and should have mixed type teams.
~Get rid of Triple/Rotation Battles:
Double battles are fine, Triple and Rotation just feel gimmicky to me. Keep things simple.
~Veteran Modes:
An option for NO TUTORIALS!! I've been playing since RBY If I don't know how to catch a Pokemon by now, I never will.
Hard mode: Increased trainer Pokemon levels, Wild Pokemon stay the same, Items cost more, battle handicaps which increase your prize money.
Just a few things I want to see :)