I think having the option would be fine, as long as there was a way to make the play experience similar with both control styles. Metroid Prime's control style on the Game Cube used different things to allow for some run and gunning, but it was still mostly exploration based.
I think if Metroid Prime were remade, you'd have to relegate the C- stick controls to a button. Metroid Prime 3 fixed the problem by allowing the weapons to stack like in Super, Fusion, and Zero Mission. I think a dual analog solution could work, but I'd have to feel the button configuration before I could make a final judgment.