If Portal 2 taught me anything, it's that Valve has no problem retconning things for the sake of gameplay. All the vagueness of the series thus far will probably be manipulated or ignored in an epic, super-QA'd fashion. No matter what they do, it will be entertaining.
The way things are getting drawn out, there's no way Valve can live up to most people's impossibly high expectations. They've written themselves into a corner, but I trust them to find a way out. Even in 2's episodes, they were struggling to find new things to do with the scenarios and writing. Valve will innovate as they always do. Be patient, people.
All I ask is that they deliver a long, challenging shooter that finally answers who or what G-man is, and what his motives are, and brings the series to a satisfying end. Any part of the story they need to change to do that is fine by me. And it kind of has to be a full-fledged sequel rather than an episode. Evolution of the story should be expected.