Samus Aran was never a strong female character.

In the first Metroid game, the player controls the character of Samas Aran. Only at the end is it revealed that the character is female.

"We were partway through the development process when one of the staff members said 'Hey, wouldn't that be kind of cool if it turned out that this person inside the suit was a woman?'" Link1

Let's sidestep the pink bikini for just a moment, I'll tackle that a bit later. Samus' sex was irrelevant. An important distinction, and one that I think was indeed kinda cool. But over the years this aspect of the game has grown to ludicrous proportions.

Which brings us to Other M. Where overwrought and possibly sexist storytelling portray Samus as a weak woman who seeks the approval of a man. And the argument has been made that Samus' relationship with Adam is dysfunctional. Link2

What's the nature of that dysfunction? Is it... Sexist? Is it... Misogynist?

I'll give you my take on it. It's a fantasy based on fanboy perceptions of what a strong female character should be... male.

Yes. Our perceptions of agency are male-centric. In order to be percieved as being strong, a female character acts in ways typically viewed as masculine. "Kicking ass and taking names."

But.

This clashes with our real world experiences of the feminine. Most women act through others, and avoid direct conflict. Those that do stand out because of their rarity. (Please lay your opinions on Thatcher's politics aside for a moment.)

So we have this odd clash of typical feminine behavior, and fantasy female behavior. And it implodes spectacularly in the story of Other M. Where Samus defers to Adam's authority with little reason and no sense of self-agency. This is a story by men for men about the "strong" woman fantasy. Samus kicks ass at the direction of a man.

Remember the pink bikini? 

The Zero Suit is Other M's pink bikini. Again, it's an appeal to the male fantasy of a sexy woman, acting like a man so the fan can feel better about ogling her butt. The mishmash of feminist guilt versus male sexuality. Just ogle her goddamn butt and get over your societal induced shame of your sexuality.