They might have pulled such a self-doubting personality with these strange emotional attachment issues off, continuity or none, if they had written it well. But as said, it was pretty dire in that respect.
And the ironic thing is, like I mentioned a long time ago, I don't think it is THAT big a deal either, as you can still just try to enjoy the game and Metroid doesn't have a narrative tradition that people have normally enjoyed that this game would contrast badly to.
But that doesn't excuse tying to pretend it is in continuity when it so plainly is not.