Seems most people think there's nothing actually wrong with Other M's controls and since most of the complaints posted just seem to be about the story, I guess my question has been answered. Seems the answer is 'The 3DS won't be fixing any control issues as there are no control issues'
No, there are actually a lot of control issues, and no, they couldn't be fixed by putting the game on the 3DS. For one thing, the 1st person mode is fundamentally broken, there's no way to aim attacks in 3rd person mode, and switching from 3rd to 1st will still be unnecessarily disorienting. The idea shouldn't be to make Other M work on 3DS, the idea is to forget about that game forever, and for Retro--or someone competent--to make the next Metroid game, no matter which system it goes to.
Team Ninja is pretty much incompetent, and wildly ill-suited to handle the Metroid franchise. Their brainless button-mash gameplay, extremely disrespectful view towards female characters, and lack of building logical, deep, and atmosphere-rich games did nothing but smear a disgusting blemish on the Metroid franchise, and Nintendo as a whole.