l like your idea @JonM, nice work, and a great summary of the movies into a game.
As for linear or not, I had an idea for ladder style set of rules (similar to GB) for a custom game so linear but encourages everyone to play all 3 balls as it is also allows the player to jumble.
3 modes in 3 ladders
mode option is triggered by a feature like a skill shot of similar to slimer on GB
Ball 1 - opens up the first option of each ladder. If all 3 are completed the second option is opened up early.
Ball 2 - opens up the second option of each ladder. But then on completing a 2nd rung of a ladder, the first rung will then flash making it possible to complete that if it wasn't completed on the first ball.
Ball 3 - opens up the third option of each ladder. But then on completing a 3rd rung of a ladder, the first rung & then second rung will then flash making it possible to complete that if it wasn't completed on the first & second ball.
Bonus points if you complete the ladders in order of the ball.