You make alot of interesting points. Bringing the series into third person would be awesome, but would have to be executed in such a way that the transition from 2D feels more natural instead of jarring. I also agree with you on the characterizations of Mother Brain and Ridley. They are essentially monsters and should be feared as such. And a big time YES on the different Metroid forms being more present in the games. I get that the larval stage of the Metroid is more iconic Nintendo but the later Metroid stages are far more creepy in my opinion and much more difficult to contend with (easy to see if you played Metroid II).
I'm honestly not so sure about their being audio logs though. Reading what an alien species has left behind on your own feels more foreboding than hearing them talk about it. The Zero Suit also never really bothered me. It does cover Samus' entire body so I fail to see how it's sexualized. And let's face it, if Samus were to take the Power Suit off or whatever, she would have to be wearing something skin tight so her clothes don't get in the way. The picture you provided could make a reasonable substitute however.
All in all, you made some awesome points though. If the series were rebooted in this fashion I would be all for it.