I would actually prefer not to play as Samus anymore, but a custom character. Hearing the fanboy boners wilt as if thousand blood vessels screamed and were suddenly silenced since Other M has killed my enthusiasm towards the character, who can only ever again be portrayed as Master Chief with boobs or else somebody rages over it for one reason or other. The cultural position of Samus is so pedestalized that it should translate better to a near mythical figure in the game as well.

On the other hand, if the plot attachment to MC is just "wants to be Samus Aran", that could yield a pretty functional trapping for a silent protagonist. A lot of options to railroad the plot without breaking immersion, like NPC's could be read as being presumptious and that would only play into the introvert bounty hunter shtick. Or the whole being a gurrrl shtick.