The CoroCoro scans confirmed that it takes place only 2 years after BW. In the
official trailer, the villainous team uniforms are quite similar to Team Rocket's, so this is very possible.
My theory is that the new scientist character is at least morally ambiguous if not a villain, due to his character design, the details about him so far ("mysterious," researching pokemon strength, etc), and the fact that he is not named after a tree or plant. And that Hilbert/Hilda will replace Alder as champion, and change depending which gender you're playing as, or will at least be fightable.