I don't think the lack of choices is necessarily a bad thing. The original Doom had no story choices (it barely even had a story) and it's still pretty good even by today's standards. Half-Life 1 and 2 pretty much had no story choices as well (there was 1 at the end of the first game) and the first one in particular is considered revolutionizing how stories are presented in games.

What I do think is an issue is when the game presents you with a choice that doesn't matter. Bioshock Infinite is the first that comes to mind as the game puts quite a few options front and center, but really none of them matter (except the very last one) and the game even implies that the choices deliberately don't matter because "constants and variables". Thus those choices, at least for me, detracted from the story because there was never no need to make me make a choice.

In that sense I agree that choices should matter, but I think a better wording is that if you're going to have choices make them matter or don't have choices in the first place.