The way Samus started out, her character was incredibly boring. By today's standards, at least. She had zero feminine traits, and could just as well have been male as female. But for her time, she was an interesting character. Back in the 80s, women had to prove that they could do the things men do. A strong female character was one who could do what men do. And that's what Samus was.
But as time has passed, a strong female character had to be more than that. It's today more or less commonly accepted that there is little difference in what men and women can do. Samus' character is more or less redundant, because the point that her character - and character like hers - was trying to make, has now already been made. There's no need to make it again. For a strong female character to be interesting today, she has to be more than just strong. She has to be cunning as well, and - preferably - show sides of herself that a man couldn't, or would be harder stressed to.
I probably don't know the origin of the zero suit well enough to speak of this, but I'd imagine that this could be a part of the reason for why it was made. As "Super Samus Aran" she isn't interesting anymore, but if you removed the "Super" bit for a while, you could make her interesting and relevant again. I'd imagine this was also the reasoning behind Other M, although I obviously can't know that.
So, I disagree with your ending sentence of your opening post. Samus has been a great female character, and Nintendo is trying - and struggling - to keep her being one.
