I'm interested in what you mean by that. I'm assuming it's from a story telling perspective rather than a gameplay one?
Other M obviously takes a great deal of gameplay inspiration from Fusion and incorporates it loosely with the Prime trilogy.
It is, without a doubt or argument, Super Metroid. The game is a textbook example of how to incorporate open-ended level design with a sense of unknown exploration and slow progression via gradually empowering the player. It also was masterfully able to implement sequence breaking that was only...