I'd say no Banjo at Microsoft may be an indication of no Banjo in Smash. Could have all been group think. While I'm expecting something Banjo to be shown at E3, either from Microsoft or Nintendo's conferences, I anticipate nothing happening, which is a possibility. Ideally, Microsoft presents a tease for Banjo's new game, followed by a tease of Banjo in Smash, Bowser comes out on stage to talk about their partnership and to watch their Direct for more info. Though given Sakurai's statements, I doubt that'll be the case.
But I agree, out of everything, I just want Banjo in Smash. But I'm not rooting for nothing at Microsoft, as I want more from the bear and bird, just not expecting it.
Good luck, ya'll!