I disagree, the mystery, nor the "truth," was not supposed to be fully uncovered...
Half Life 2 is not Half Life, so you should not expect everything to be similar - just look at Team Fortress Classic and Team Fortress 2 or Kot0R and Kot0R II.
Again, the game is not, to quote our favorite reviewer, "Half Life: Citrus Cannon" or "Half Life: More of the Same," it is Half Life 2, the continuation of the Half Life plotline. Go join the Black Mesa mod team or buy Half Life: Source if you want a clone of the original...