I think I remember reading an interview with the dev team where they explained that playing action for too long was boring, as well as solving puzzles, so they consciously designed the game with interleaved phases of action/puzzle. Your recompense for solving a puzzle is action, and your recompense for killing all the bad guys is a relaxing puzzle.
It's funny you didn't liked that, because for me it was the complete opposite. I like pure action shooters, and I like pure puzzle adventure games, but I really loved Half-Life and I didn't know why until I read that explanation.