Siliconera: "People love LovePlus. People also love the 3DS. And hey, since people also love money, you’d think that’s reason enough for Konami to already be working on a 3DS-compatible successor to the game. Either way, 428 director — and he’s also part of Level-5’s Time Travelers game — Jiro Ishii feels that, such a project, if it were to exist, would be dangerous."
This image basically confirms that in Ultra Sun/Ultra Moon we will be seeing an alternate story. While it has been stated by Nintendo multiple times that this was the case, they were never really clear on it.
Hey! Pikmin is brand new adventure set on the Nintendo 3DS as Captain Olimar's ship crash lands on a mysterious alien planet.