My dream sequel would be a continuation of the Metroid Prime series.
Drop the tank controls, opt into fps controls. Seamless huge environments. I want a Halo CE game with Metroid mythos and traversal. Give samus vehicles and federation troops to support the fire fights. She would use her power ups in large areas! Imagine the super dash and spin jump possibilities.
Eliminate the double jump, opt for high jump. Last but should be first. 5(!) missiles to open red doors.