I expect a previously unknown retail title to hit in late 2017 on less than six months' notice (unless Rabbids Kingdom Battle was meant to fill that slot, but I think we can agree that neither it nor FE Warriors are coming out of the first-party pipeline), but I don't think it will be either SSB or Pokémon. Between MK8D, Arms, and Splatoon 2, this is already the hardest Nintendo has ever pushed first-party online multiplayer, apparently to the end of pushing the paid online service (and sweetening the deal with "free" post-launch content for Arms and Splatoon that keeps players engaged, with the online fee subsidizing said content), and I don't think it's to their advantage to drop SSB Switch too soon, even if they're hanging on to a title that is ready to ship. I'd sooner expect it to be their all-audiences flagship for the first half of 2018.
Rather, I'd expect something like a principally single-player experience that doesn't fill the same role as Odyssey, Xenoblade, or the BotW DLCsomething comparatively lightweight but not to the point of being multiplayer/online-centric. FE Warriors is arguably that kind of game, but I'm thinking along the lines of Animal Crossing, WarioWare, Mario sports, or a 2D platformer in a minor series (I'd say Kirby if the IP didn't already look so busy on the 3DS). These are all titles that would be well positioned to round out the library and cover all bases going into the holiday.
By the end of E3 I expect to know about (a) one new retail title for late 2017, (b) at least one title for Q1 2018 (which may be Xenoblade 2 if it doesn't make it to the west this yearthe big tell will be whether we see any footage with English text), and (c) the mass-market tentpole for next spring (SSB would certainly fit the bill).