It's not that I think Retro doesn't have something cooking, but for a 30 minute presentation in the first year of the system's life I don't think they're going to show it. They revealed all of their 2017 big guns for Switch earlier in the year as part of their effort to hype it going into launch. If Retro had something earthshaking that was ready to show in a meaningful way as of E3, I feel they would have shown a teaser in Q1 rather than hold it for now.
It's definitely not impossible something will show, but 2018 feels right for their next game and the Switch selling well means there's not any incentive to announce games that are quite a ways off. A direct in Q1 2018 would be fine for a Q3-4 game.
I'm expecting perhaps one or two surprises at most, and those will probably be on 3DS. Most of the direct will short clips of their already announced 2017 slate.
Retros game is always first shown at E3, the only other big Switch event was a live Japanese show it would not have been shown yet, now is the time