I think the problem is that people are saying "it doesn't fit her personality" despite her not being given any major character traits and what not in Other M, previously we all thought of Samus as some battle hardened vet who only lived to complete her mission,, however in Other M we were shown more of the soft side of Samus, we saw her fear, her anger, her sadness, those represent her feminine qualities. In smash 4 she still as as Stoic as ever (from what I see), however, because smash is a fighting game and Dialogue isnt major in it, in order to represent Samus' femininity Sakurai chose to giver her heels, but at the same time not majorly contrasting from her combat prowess (hense why they are rocket heels). At the end of Other M we saw that she was not just a Kickass bounty hunter, but also a woman and it would be unfair to ignore those parts of Samus in smash