I feel like there's a pretty solid chance we'll get a female evil team leader. The devs seem to have been increasingly conscious of the diversity of the story's cast. They've done a good job at portraying powerful, malevolent female characters (nearly every organisation has at least one strong female admin) so it'd be great to finally have one in full command, and I think it's pretty likely considering how mindful they are of that diversity.
Different races appear more frequently now without any kind of stereotyping, we've had plenty of female champions, so I feel like this is their final step logically.
It'd be exciting to know from now on we can expect any role to be filled by any kind of character.
I also think it's possible that they'll bring back an old team. Can't see Aqua/Magma making a return (despite the sun/moon connotations of their plans) since both teams learned their lesson and there's not much more story you could pull from their ambitions.
I can't see Team Rocket being majorly successful in a new region because how incredibly everything fell apart for them plus their schemes weren't so grand as to do anything that might affect the sun or the moon. They just wanted power and money.
Team Galactic and Team Plasma I could see returning. There were enough loose ends and they were both ambitious enough to take to another region.
Though, if a team was to be reused it would probably be Flare because of how many loose ends there were and how their plans could pretty easily be pursued in different ways. I really hope we don't see much, if any, of Team Flare though... That might just be me but it was easily the most boring villainous team to date, personally.
As for the evil team (whoever it is)'s plan, I can't really see it being anything to do with shifting the sun or moon's location considering that hurtling the earth towards
one of these was the plan of the antagonists in another (spin-off)
pokemon game. Only look at that link if you're unsure what game I'm talking about and don't mind a bit of a spoiler if you haven't played it.
Maybe they'll attempt to harness the power of the sun or the moon? Perhaps put something on the moon to channel the sun's power into a weapon that can be aimed anywhere on Earth due to the orbit (this might be a bit similar to Flare's plan, though). Or maybe the sun or moon has some mystical power in the Pokemon universe. Between moon stones, sun stones and a lot of pokemons connections to both I wouldn't be surprised.
I really hope the moon isn't a big old mega stone, though.