One kudo is that Team Ninja knows how to model people better than Retro. Retro does everything else fantastic except for humans.

But to be fair, are the characters in the Metroid universe even humans? They are definitely human-like, but I was under the impression this took place in another galaxy or something, so how do we know they are human (as in Homo Sapiens)?
They're mostly fine for what the engine was doing, with character designs by Western artists (the game focused on environments). Compare Prime 1 Samus (pretty icky uncanny back then) with Eternal Darkness people for a history lesson.
This is different from a 1-on-1 fighting game or the REmake where tons of attention had to be paid to 3rd person character presentation.
And really, Prime 3 Samus didn't look bad with those slightly aggressive eyes, dribbling neon goop from her lips.
Where's the real Metroid, Metroid Dread?