Metroid: Other M "done right" in my mind would be... well pretty much the only thing I would suggest keeping would be the third dimensional view. I liked jumping around and shooting things. The way Samus controlled was overall fine, except the first person aiming which I felt was really clunky and hard to use in the heat of the moment. I say the first person view should be ditched outright.
So they would have to ditch the shitty storytelling, and the linear progression, and the focus on action over exploration and then you're probably fine. So you're left with Super Metroid with polygons? What the hell did they get even remotely right with Other M? It's like everything it introduced to Metroid was a clusterfuck disaster.
There is nothing wrong with moving forward. But when you step forward into a pile of ****, you step back, clean off your shoes and head in a slightly different direction.