It's gotta be MGSV, if only because it's a franchise where I really expect something special from the story (even if I don't like it as with 4). It's to the point where it even stretches the definition of "disappointing story" since it barely even has a story at all, there's simply no attempt to tell a good one. It's the "the bad guy is here, go get him. Okay, now he's here. Okay you're done now" kind of justification-for-action you'd get in a NES game.
It's not necessarily a disappointing story overall, but I did think Life is Strange left me a little cold at the end. It's not so much that they didn't stick the landing, I think they mostly did (it has a willingness to put its characters through the wringer that not many other games have), but looking back from the end, a couple shortcomings that had been there for the whole thing became a little more apparent. I hope season 2 has a stronger protagonist.