Quoting Nintendo Life's feature on Metroid: Other M:
"The biggest sexism argument seems to be the fact that Samus is forced to submit to a man's authority. Interpret it as you will, but let's not forget that she views the man in question as a father figure. The game tells us that she submits to him not because she's forced to, but because she wants to prove to him that she's not the immature, authority-hating youngster she once was. It may read in part as sexist for a female youth to feel this way, but to disregard all other aspects of her character and reduce her to her gender for this interpretation is a bit sexist as well. Still, it's not a completely closed case: Metroid Prime 3: Corruption and Metroid Fusion both place Samus in a situation where she is forced to obey orders from a male (or in the case of Fusion, a computerised male) officer, yet somehow both these titles managed to slip past the ol' sexism radar and gain huge amounts of critical acclaim. At least Other M tried to give a reason as to why she decided to submit, something that even Corruption failed to do. There's nothing inherently sexist about submission or self-doubt, and the notion that female characters must always avoid both to be considered strong is a bit sexist in and of itself."