one way, albeit one that would require a lot more work, would be to have it so that the scripted sequences could play out in different ways. ie, you have two or three versions of the same scenes. not necessarily in a branching fashion but in a swap in and out fashion. it's still essentially plays the same, but it feels less linear. give the player subconscious choices every now and then, and have gameplay scenarios scripted for whether they went up the stairs or down the corridor.
but i understand why almost no one ever does this, because so few people would see all the work you'd put in. polishing ten hours of linear gameplay is a lot easier than polishing thirty hours of gameplay that each player will only experience ten of.
i don't think however that every game has to appeal to everyone. the audience that don't mind this 'issue' are clearly large enough for the franchise to be a success. that doesn't change the criticism from being true of course, nor should it gag people from voicing it when it continues to be the case in subsequent sequels, but since most gamers and reviewers won't mind (i know i won't), i'd rather ND catered to the wider audience than the smaller one.
i'm pretty sure they can stomach getting the odd eight out of ten from a handful of reviewers much more readily than some of the people in this thread seem to be able to.