The following text is all speculation and ideas; none have been confirmed or made official.
After Black and White 2 have been released, where will Game Freak and Nintendo head next? Their current trends would suggest a remake of Ruby/Sapphire/Emerald before moving on to Generation VI, but, as they were less popular entries, perhaps they'll leave them alone for now. I'd actually love to see them remade, as I feel Game Freak could apply what they've learned since and make them far superior games to the originals.
Whether there is a remake or not though, Generation VI is inevitable. There's also little doubt that it will be released on the 3DS. And, let's face it, combining 3D with Pokémon creates some tantalising possibilities. If Game Freak wanted to rejig the battle arenas a bit, watching attacks fly from one Pokémon to another with real depth would be quite impressive, or watching a pokeball fly towards your target. Massive cities like Castelia would be more impressive, and even watching a legendary Pokémon fly down (a la Reshiram/Zekrom) would be awesome.
Through the Pokédex 3D app, we've already seen what Pokémon look like in the real world using AR, but what if this was applied to the main series? Perhaps the trading cards would come with matching AR cards that could be scanned to catch that Pokémon in game, or simply to see them pop up. Playing the card game in combination with a 3DS could really bring Pokémon to life. For those of you who have played Kid Icarus: Uprising, you already know about the technology to make cards battle each other. It's still primitive though, so hopefully they would do some further development on it first.
What else? Personally, I like the 2D sprites, but 3D is a possibility if they did it well; multiple save files would be a dream, but I think we all know this is never going to happen; a change in the Grass/Water/Fire starting Pokémon trio (Fighting/Dark/Psychic, anyone?) might be nice; or even a way that Pokémon can learn HMs without them replacing a vital move (free the HM slaves!). Perhaps even great ideas that were done in earlier generations but forgotten in V could be resurrected, such as the Underground, gym leader rematches, and your lead Pokémon walking beside your trainer.
There are tons of improvements and features the Pokémon developers could work towards and implement, but I guess we'll just have to wait and see what direction Game Freak takes it in.