Speaking of, how would you guys feel about, in the next Metroid game (hopefully by Retro) that there would be a Ridley tunnel-shooter based mini-game? Blowing up galactic fed ships with your fire and slashing your way through steel and space debris? Separate from the main game of course. Either that or weave in TPS/FPS/2D Sidescrolling Samus action with Ridley tunnel-shooting action two have two stories going at once, where they intermittently cross each other for a fight between the two. It would certainly be a great way to introduce the fact that Ridley can talk with sadistic banter with his long time rival.
The final fight would likely be two parts. Probably some super enemy that proved to be a threat to both the Space Pirates and Galactic Federation, and Samus and Ridley decide to attack it at the same time, and once that baddie goes down, you choose either Samus or Ridley to end that final fight as they clash against each other one last time, which influences the ending (With Samus's side likely being canon, of course).
Regardless of your feelings on the game, it reminds me of the dynamic in Ultimate Spiderman, where you alternate between Spiderman and Venom: