That's just the thing, isn't it. I hear many criticisms regarding how "predictable" LiS's ending was, and I can't help but wonder why people think that's an incredibly valid criticism. Sure, the game had already had more than a couple interesting twists that formed their expectations, but I still don't think it's unreasonable for a game to address the problem it poses in its beginning directly and predictably.
Would they have preferred it if Chloe started to regale Max about the troubles with Synthetics and Organics? It'd certainly come as a surprise.
I think the "your choices matter..." disclaimer gives people the wrong impression about this game: like it's supposed to be about choices at its core rather than simply use choices to make a different point. LiS had a clear message it was trying to send, and it did that. I don' think adding in extra choices or crazy twists would have helped.
While I almost began a truly impressive rant on why I hate MEHEM and consider insulting to a insane degree, I mostly agree with you here. Especially on the predictable part, except I would really like them to explain how they were able to predict the path to that point so well.
I also think you are on the point about the incorrect, for me, perception of what it means for the choices to matter. Each choice you make in that game defines Max as the game is ultimately about her, and to some degree Chloe's, growth in to adulthood and as a person. Various characters in the game comment on how different Max seems as a person due to those choices. Ultimate, for me, a happy ending where everything goes great would have been extremely disappointing, not because I want things to be sad, but because one of the central points of the game is that there are rarely easy choices and being an adult is to do what you think is for the best and carry the responsibility for that. Having a 'you win' ending would have hurt it so badly.
By the way, which again ties it to ME games as it raises the fair question in that is a 'you win' ending truly the best solution for all stories/