Part of why many people don't often get the story, is because in most games, they just tell you everything and you don't have to think about the story but in hl2 you have to draw your own conclusions. There happens something and the game doesn't exactly tell you what/why/how etc. You have to think about it yourself and then come up with an answer that makes sense.
The narrative is just different than in most other games. A big part of the story is told through the environment. Let's take for example, the chapter "Highway 17". You drive along the coast and look at the "beautiful" scenery but what you see there is strange, a lot of stranded ships and landing stages far above the sea level. It shows that the sea level has sunk quite a lot in a very short amount of time. Thanks to that you can come to the conclusion that the Combine destroy our environment and need a lot of water, for whatever it is that they're doing (some even say that it's a warning from Valve, to look more after our environment or something like this will happen). Many don't really think about it or barely even notice it and just drive past it.
Another example from "Highway 17". A house is standing beside the road. The game lets you choose, you can just drive and leave it behind you, or you stop the car and go inside it. The house looks deserted, the windows are boarded and the front door doesn't open. On the wall there is a skull sprayed. This shows that the people try to tell others that the house is dangerous and no one should go inside, it's "infested". Upon entering, you get attacked by zombies and after getting rid of them, you look around. You see beds, cupboards, pans and other thing. Now you start to wonder, who lived here, what happened to them? Was it a family, or an outpost of the resistance? It's a perfect example of the cruel way, the Combine use to get rid of people from places, where they don't want them to be. They just shoot the headcrabs inside and then leave the rest to them. Now you're left to wonder, how many people made it out in time, if any at all.
Let's take something much more subtle and insignificant but something that I really like about the narrative. Right before you encounter the Manhacks for the first time in the sewers, you meet a man in an outpost from the resistance and then you two get attacked by the Manhacks. After fending them off, you go on and that man stays back. Shortly after that, you meet again some Manhacks. Now, after destroying every single one of them, most people move on because there is no reason to turn back. But if you do head back to that room with the rebel, a Manhack attacks you, even though you destroyed them all. It must have come through the way which you first entered the room from. Now again after blowing up the Manhack, when you look down, you see the poor guy lying dead on the ground. Most people easily overlook this and who could blame them, the game doesn't give any reason to go back to this room. But just because of that I love this scene. It just shows that you and your immediate surroundings aren't the only thing in the world, things continue to happen even if you don't witness them, they happen almost simultaneously with your actions and the game doesn't tell you at all that this occurred. It just goes unnoticed unless someone tells you about it, or you go back for no reason.
All this, combined with the personality of Gordon Freeman (won't talk about that now), leads to something else that's really good about Half-Life 2. The game is very personal. Everything that happens there, everything that you experience, is your own experience. No one else has it. Only you played the game that way and thought and looked at things that certain way.
I could now go on and on, about the atmosphere, the immersion, the characters, I could write another post with this length about the G-Man alone but I won't. I don't want to force you to like the game. I just tried to show you why I love it so much and why it got so much praise.
I think part of the problem is, that it has been praised so much, that a lot of people expect something entirely different, something like Mass Effect (not that I wish to imply that Mass Effect's Story isn't good) but then they play it for the first time and get disappointed because it wasn't what they had thought it would be.
Of course it's entirely possible that Half-Life 2's style is just not your cup of tea. There doesn't exist something that everyone likes.
