I know people who tell me they can't play FPS games because it makes them nauseous and gives them headaches. That's probably not a common problem, but apparently it does effect some players, so by restricting a game to first person you are cancelling out a certain demographic of potential gamers.
Not to mention the fact that FPS games do not sell over in Japan at all, so if you have a game in 1st person then it is pretty much guaranteed to bomb over there. If Nintendo wants to boost the appeal of the Metroid franchise in Japan then having it in 3rd person is mandatory. Since Sakamoto is Japanese, he probably would refuse to ever make the game in 1st person anyway, so I'm not particularly worried about that. I don't have any faith in Sakamoto to make a Metroid game of the same calibur as the ones made when Gunpei Yokoi was still alive, but at least I believe he would keep them in 3rd person and that is one thing about Other M I'm not complaining about. Many things suck about the game, but I'm cool with that part of it at least.
As for aiming the missiles in the game, I like what is done in Fallout 3 and Fallout New Vegas with the VATS thing where you can target different enemies and even different parts of the enemies. When you're in VATs and taking aim the action slows down but it doesn't stop completely. This slowing down means you are less likely to get your ass kicked while you're locking on the way you do in Other M.Fallout 3 is mainly a 1st person game, but it can also be played in 3rd person and the VATS works either way so I don't see how something like that couldn't work in a 3rd person Metroid game either.
But I don't see why it can't just be like in the original Metroids except in 3D. Samus can move with one analog stick and independently aim her arm cannon with the other analog stick, and one button can fire an energy beam and another can fire a missile. What would be wrong with that approach? I admit you lose some pinpoint precision by doing this in 3rd person, but Metroid isn't meant to be played like you're a sniper in COD so first person precision really isn't necessary. The bosses you frequently need to use missiles on literally fill up the entire screen in many cases, so hitting them isn't hard (although hitting their weak spots conceivably could be).