Reboot the series. Like, scrap everything and start from scratch on 3DS or Wii U. Keep the story to a minimum inside of the games. If you really need to explore Samus' origins and her feelings, do it in some manga or whatever. In the games she should be simply a vessel for the player to explore the game without exposition or characterisation. The setup for every single entry should be simple: The Galactic Federation wants you to check something out, go to that planet. Oh no, Metroids! Don't bother with an overaching storyline, I doubt anybody cares. Of course, introducing enemies like Dark Samus or SA-X shouldn't be out of the question.
Make it look and sound unique. Metroid should be a bit scary and atmospheric without being gritty and brown. Other M had good designs for many enemies, just be more smart with the colour. Use moody and memorable music, not just ambient sounds. It's okay to make the player feel like a badass from time to time. Look especially at Super Metroid for this.
Keep it 2D or at most 2.5D without any touch, motion or 3D gimmicks, just a huge, interconnected world to explore. Emphasis on world. No stupid space-bases, I want a planet where you can see that ancient civilizations lived there. Upper screen/TV for the game, lower screen/Wii U Pad for map. Otherwise, no directions, no cutscenes, no dialogue, just no bullshit that takes me out of the game. Tell the story through the environment like previous games did. Bring back the scan function from the Prime series but only to tell the player more about the world, not as a part of the gameplay. Concentration mode from Other M would be preferable as well; it's not fun farming enemies just to get one full Energy Tank.
The two pillars of successful Metroid design for me are exploration and achievement. The world has to be both mechanically as well as aesthetically encouraging to explore with sequence breaking being a viable but challenging part of the game. It's 2013 for crying out loud, get inventive on how to make environments that are fun to explore by their own without making up arbitrary objectives. The game shouldn't have to tell me to go somewhere, it should make me want to by myself. Whether they do that by putting in challenging platforming sections, puzzles or just interesting architecture doesn't even matter. The other aspect, achievement, is a bit of a no-brainer but still worth mentioning. Almost everything in the game should be caused by the doing of the player, not the game, not some enemy, not a supporting character, not even Samus herself. I should be able to say "It was me who did that". Found my way through an intricate maze to get to a health-powerup? I did that. Killed an enemy by making the ceiling of a cave fall on him? I did that. Made ancient ruins rise from a barren wasteland? Yup, all me. It's the player and his motivation who should be the driving force in a Metroid game. I push the events forward, not the other way around.
) demand that all devs spending their female charas something better. But there is nothing wrong with hoping Samus makes the first step 
