Named after Metroid Fusion which I consider one of the most egregious examples.
The tendency for a videogame series that has lots of exploration and non-linear level design to develop a more structured story and in response curtailing the non-linear gameplay in favour of a more linear design.
For example, Metroid 1-3 had very little story, you were Samus Aran, you got to kill the mother and in the end you fly away. Fusion suddently decided to add characters, story development, etc but to tell that story it locked the player into a very narrow path, making sure there is no way to stray from it and ruin the story. The Prime series was similar, Prime 1 was mostly about the environment, Prime 3 had tons of mission goals and story cutscenes.
Mario 64 had a very freeform approach to levels. You could waltz in and take the stars in almost any order, your only goal was to get a specific count to unlock another set of levels. There were three mandatory levels where you fought Bowser that were the entirety of the story development. Super Mario Sunshine: Suddently there's this unknown enemy whose identity is revealed by the story later on. You're forced to beat the stars in a fixed order and in order to complete the game you must complete seven stars in EVERY area. All the other stars were of no use for beating the game.
Zelda 1 and 2 had almost zero story, you explored the map and beat dungeons in almost any order you wanted. LttP had more story and a somewhat more restricted level order (though you could still take them out of order). Ocarina of Time wasn't even coded to cope with players sequence breaking and beating the temples in a different order, since it's designed to be completely linear in its overworld progression it only checked if the final temple was beaten to unlock the route to the boss.
Symphony of the Night was very unguided, there wasn't much that was necessary for moving through the castle, only a few items were necessary for accessing about 99% of the castle. I didn't even figure out the high jump boots until after I got the bat morph and could just fly anywhere. The GBA games had a harder sequence and breaking it was very hard. PoR had the pictures that took you into different worlds, kinda like the sectors in Fusion. Ecclesia lost the freeform completely, almost all levels are just glorified corridors with a single route through them and only a few treasure rooms attached.
Those are just the first few that came to my mind. It seems that story is the mortal enemy of freeform gameplay and with the hardcorification of core gaming more and more games want to develop their own stories over the gameplay that they started with.