It's a weird hypothetical that's kind of hard to imagine. If the game truly bombs - e.g. 1-2 million sold after all these years of development, that'd be pretty awful
1. The investment into Retro Studios would be over, or at least they wouldn't be able to function with any level of autonomy. We're already at 6-7 years without a new release, and several more years to go.
2. Metroid games might still be developed because the IP is pretty unique among Nintendo titles, but we may just see 'safe', less ambitious 2D releases for a while.
That said, I just don't think there's a real chance of the above. I cannot see them cancelling the first version, pushing it to Retro, and still putting out a bad game.