Setting and the Physical Language of Puzzles

I'd like to clarify my use of the word "should" in the last post. Game areas should form a cohesive game world iff this is a goal of the game design. Functioning worlds (by which I mean worlds that appear to have feasible ecosystems, economies, etc. within the fiction) are not important or necessary for all games, certainly; it's not a good idea to try to limit possibilities here. For a game that seeks to immerse the player in its world and/or story, which very many games try to do, the world should make some sense, or it will detract from the immersion.

To go back to my Metroid Prime 3 example: would MP3 be a better game if this imposed interface were more blended into the world, if it made more sense for those spherical crevices to be there in the first place?

I'm not convinced it's even possible. One gameplay component of Metroid Prime is the puzzles, and to have a good puzzle, you need to set up the physical language that the player interacts with and can "read" to solve the puzzle. The different devices in Metroid Prime, for example: the player sees a small glowing circle and learns, from the tutorial and from doing it over and over, that when they see one of those circles, they're supposed to turn into a ball and drop an explosive in the hole. In this sense, puzzles in Metroid Prime are simply a matter of reading the symbols.

(Similarly, The Legend of Zelda develops its own language with the player: the player learns that a certain target will stick to the hookshot; how far Link can jump or if he has to use the hover boots; what rocks can be blown up with bombs; and so on.)

The point is, if the various technologies on each planet were more unique and made more sense, it would obscure the puzzle language that is very clear the way it is now. If that were to change, at minimum it would be the same problem with a thin layer of paint over it, causing some frustration for the player while not enhancing immersion at all. At the extreme it would cause gameplay that requires the player to relearn the same simple activities at every planet, and not allow the player to reuse knowledge from the last world, limiting the player's sense of advancement. So in this case, making a more "immersive" universe in this sense would be detrimental to Metroid Prime 3's gameplay.

I get the feeling the environments in Metroid Prime were designed more for cool factor than immersion, which is totally fine by me.