I honestly think that they've written themselves into a corner with the story.
As the series has gone on there has been more of a narrative and more "key" characters and interactions all hinting at something big.
The two main problems are, firstly, I don't think even valve know what the big link between all the plot elements is going to be yet - it's been put on a pedestal (all this talk of aperture, black mesa, g man, advisors, vorts etc). Second, they have a silent protagonist, this can't make things easy when every other character talks chats away, explaining plot points, yet the main man can't ever be a part of it.