Well, to start, what Guy said.

But also, the company couldn't finish the story. They could not move forward because so much had happened and they didn't know how to continue. They had an ending for the episodes, but that just twisted things more. Level design became so important they were hiring actual architects and people with knowledge to design areas to actually feel like the area.

There is a feeling that it needs to be better than the previous game, so they have scrapped more version than we have any clue about. They scrapped stuff or changed ideas for Half Life 2, and that was fine, so it felt right to keep seeking a greater form of perfection. Because of that, nothing was released.

The creators of the game have slowly left the company. Apparently the older members still demand it be this great vaunted thing. Tons of ideas have been scrapped. Heck, I'm fairly certain there have been several versions of Source Engine that had various Gordon Freeman ready to not talk. Newer members are going in a new direction, but that is still rare and feels kind of weird.

Half Life 2 was so good, no one knows how to continue it. It defeated itself.