Yes, alot of the lore isn't readily apparent. I'm still curious what GMan is and what he wansts in the end. Too bad there probably won't be a HL3 too soon, if ever.
I think there are games today with good stories as well, just that it's harder to find between all the generic or awful ones.
I'm not much of a FPS fan myself, but the HL series is something else. It's not too cheesy, it's not too serious, the level layout is phenomenal, that even after years I can still tell you where to go to and what to do to advance.