First of all, I don't think we're getting another 5th gen game, 5th gen seems to have run its course already despite only releasing two sets of games. Just about the only thing left that would have any ties to 5th gen would be to create the Original Dragon, and that's something that could happen 6th gen. And no RS remakes, either, 3rd and 5th gen are too similar to warrant bringing back RSE yet. The graphics look too similar because 4th gen is just 3rd gen with slightly more 3D and 5th gen is almost identical to 4th gen because it's on the same system. In terms of game mechanics, the only major difference is the physical/special split, and double grass and shaking spots, and even then, that's not enough of a change. 2nd and 3rd gen brought with them much more drastic changes to the games. So I'd wait until 6th gen for that. Now then, here are some things I'd like to see for 6th gen:
-Bring back the Vs. Seeker or create a new trainer rematch mechanic that works similarly, and never remove it. Unlimited trainer rematches are always good, and I was disappointed when BW1 severely limited trainer rematches and even more disappointed when BW2 did nothing to fix it.
-Bring back Pokemon following you. That was one of the most fun changes they made to HGSS, it adds to the notion that Pokemon are supposed to be your friends and nothing beats the feeling of walking around in the world with your favorite Pokemon following you around. Possibly also make this mechanic more useful to the gameplay, such as the Pokemon following you increases their happiness quicker, or maybe even affects encounter rates in some way or something (I can't think of anything ATM).
-Revert the EXP system to the way it was before so we don't have to rely on Audinos and Lucky Eggs to train.
-Make the regional design/storyline progression as complex as it used to be. Unova was overall horribly designed since most of the areas were connected with one long path circling around the northern half of the region. This is bad regional design because it discourages backtracking and exploration, in fact in BW1, you travel almost completely in a straight line from start to finish (aside from one little detour to Relic Castle after the 7th gym). BW2 is slightly better about this, but the hexagon section of Unova still limits how complex the storyline progression can be. Better examples of good regional design would include Kanto, Hoenn, and Sinnoh.
-Include the following mechanics from 5th gen:
-Medals. Like every other achievement system in video games, medals are an incentive to go back and accomplish certain things in the game that you might not have wanted to do otherwise, increasing replay value.
-Double Grass/Shaking Spots. If brought back, they need to be careful about what kinds of Pokemon can be made available through these methods. BW1 and BW2 both pretty much screwed this up. Shaking Spots had little more than Audinos (whose only use is as an overcorrection for the crappy EXP system in 5th gen) and evolutions to Pokemon you could already catch on the route. Double Grass offered pretty much no change to the usual encounters except for higher levels and an evolution here and there, also Double Grass patches were strewn about randomly and didn't really have much purpose. It's become apparent that Game Freak has no idea what to do with them. Allowing you to catch evolutions so easily defeats the purpose of having to evolve your Pokemon in the first place. Furthermore, Pokemon that evolve by evolution stone especially should not be catchable, since they have undeveloped movesets. And especially not extremely rare and powerful ones like Dragonite or Tyranitar, what sense does it make allowing you to catch some of the most powerful Pokemon in the game? Anyway, Shaking Spots should be used to house rarer Pokemon, making them, you know, rare. Double Grass is a bit trickier, ideally it's best used for backtracking at a later point in the game (for example, the Double Grass on Rt. 1 is only accessible when you have Surf and allows you to encounter stronger Pokemon than the usual Lv. 2 Patrats and Lillipups), but other than that, I suppose it can be used for if you're trying to go off the beaten path for whatever reason (either for some sort of side area, an area that you'd need an HM for, or a shortcut to the next area), and the Pokemon can be similar to the normal ones but with a few more semi-rare and evolved Pokemon.
-Missions such as Entralink and Fes Missions.
-The World Tournament. You gotta admit, this is probably the best idea they've come up with in BW2. Being able to rematch gym leaders is always fun, but rematching EVERY gym leader (or at least almost every gym leader)? Yes, please. If they ever bring back the Battle Frontier, this should be a staple facility in it along with the Battle Tower and Battle Factory.
That's about all I can think of ATM.