Honestly, nothing.
There's nothing I love more than displaying weakness in a "strong" character. I hate unflappable, infallibly badass characters that LOL KICK ASS AND TAKE NAMES. I was glad to see Samus have an attachment to something. I was ecstatic to hear that she lost her head at the sight of Ridley. I adored that she had to be rescued. It is HUMAN to need help sometimes. It may not have been executed so well, but I love that there was a time in Samus' life when she WAS afraid of something.
Just cause she showed weakness for once doesn't mean she isn't badass. Are people so fickle that one game will make them forget about the rest?
But then, I also didn't uphold Samus as this symbol for RAWR STRONG FEMALENESS OF POWERFULNESS any more than I did Lara Croft or Kasumi from DOA. I think all that agenda-making is complete bullshit. To me she was a game character who happened to be a woman, and no more. I never attached an agenda to an 8 bit Nintendo character.
I just hate talk of the ruination of a character. Don't like it? ignore it and move on. The series was fine without Other M, and it's STILL good in spite of it. You don't have to play Other M, but it's nice to know that for people like me, there is this snippet of Samus' life where she was vulnerable and afraid. Badasses aren't born, you know.
The biggest problem, as stated before, is that this isn't a prequel to the whole series, which makes a bunch of aforementioned things look out of character.
But on the whole, I think all the IDEAS on display in Metroid Other M were excellent ones. Having narration, having cinematic cutscenes, having other characters voice acted...all ideas that, with the right studio who'd treat the franchise with reverence, I'd love to see in a Zelda game. (and I'm a HUGE Zelda fanboy.)
---
EDIT: To add to this wall of text...
It's really sad to see people react so violently to this game. The least we could do is give Nintendo constructive criticism so that they can do it right next time, instead of waxing hyperbolic about how it's signaling the death of a seminal franchise. It's only ONE game out of 8 or so; an experiment, and one that needs work, but could be great if polished. The least we could be is constructive.
What a violent cycle. If they try to do something different than the usual, people throw a hissy fit. But then, time passes, and you look in sites like IGN or Gamespot and you see lists of "Ten Things We'd Love To See in a Mario/Zelda/Metroid Game." as if they've completely forgotten that they tried a few of these things and they got blasted for it.
Can't win for losing.