I could see a soft-reboot along the lines of BW (making you only use new stuff until you beat the main story), but not a full on reboot (especially not one that kills off most the Pokemon list, else that'd make Pokemon Bank redundant and be against the whole point of it - which was to allow players to continue moving their Pokemon forward, even across consoles. We've already started seeing the effects of loadsa Pokemon, which is where they've removed the in-game National Dex to just have the one Alolan Dex, and I could see that continuing in future, making up the Dex of each generation of a mix of new Pokemon and returning Pokemon.
Again, I can see a mini form of open-world, but not the full sandbox-y style you see in Breath of the Wild (maybe more Mario Odyssey style, where areas available are based upon story progression, where you've still got a goal you have to reach if you want to be able to access a new place, but you can also explore the current/previous areas and find some neat stuff if you wish). I'd rather the worlds smaller, with more to do, than BotW sized, as it's a fairly common complaint that the world there was too big and empty (which maybe works for a world in ruin, but not what you'd imagine to find in a Pokemon game)
For the main series, I don't imagine they'll go far off the "child gets Pokemon, defeats challenges, clashing with villain team along the way, meets legendary somewhere, eventually final big challenge" formula, though they may try other things in spin-offs (though, on the subject of playing as the evil team... I'll have to leave this segment from an interview with Junichi Masuda here "I want players to play as heroes in videogames, and I want them to play fair."
http://www.escapistmagazine.com/news/vi ... ers-Be-Bad)
Anyway, depending on how long the Switch game has been in development, when it releases, and whether it is a main series game or not, I'm not sure there'll be any particular huge shake-ups to the formula, especially as it's not a simple case as developing for a console that they've already got a decent amount of experience with.