I actually think that unless a hard swerve is done with the whole plot, I think Maria will exist and still die. Kids dying in a family movie is wholly possible as long as it's done with restraint. Maria makes this easier due to the fact that she has an immune system disease and that's the whole reason she's in the space colony. Setting the scene up as more a shutdown gone wrong as opposed to everyone in the colony getting gunned down. Maria dying also can tie in to Sonic. Being adopted by Tom and Maddie means Jojo is now his cousin. "I've got a cousin, too" is a possible way convincing Shadow to help could go, especially since family has been a theme in these movies.
The thing I think will change is "Space Colony ARK" not being a space colony. ARK could be either an Area 51 desert base or a deep sea base. The latter works particularly well if they're planning to adapt any portions of Adventure 1. Also, there's various things they can do with the visual design of a sterile environment if the base is now underwater. The temple with the Master Emerald was also underwater.
Alternately, they could skip Maria and have Gerald Robotnik see Shadow as a son.
The thing I think will change is "Space Colony ARK" not being a space colony. ARK could be either an Area 51 desert base or a deep sea base. The latter works particularly well if they're planning to adapt any portions of Adventure 1. Also, there's various things they can do with the visual design of a sterile environment if the base is now underwater. The temple with the Master Emerald was also underwater.
Alternately, they could skip Maria and have Gerald Robotnik see Shadow as a son.
