Jaime: The story of Portal 2 was basically the same as the one from the first game, with added bells and whistles, and ended pretty much in the same spot. Found that pretty disappointing.
What I found disappointing is the change of ending in portal 1 in order to plug the sequel on it. I just don't like these little george lucas procedures (unavoidable on steam, of course), and, while i haven't played mass effect 3 yet, the fact that its original ending got retconned under the pressure also irks me.
To answer the OP, yes, i think that, as the technology is here, the unapproved (or unconvenient) ending of a game can easily be changed by the authors. And i expect it to happen more and more. And i am not extremely happy about it.
And when the steam principles will spread to the way we "buy" and "own" movies...