There are a lot of reasons and I think it's time to write them up, but I think HL2 was actually over-polished. They didn't follow their own rules, either, leading to a lot of "Uncanny Valley" situations.

I wonder if we will ever see Valve recognize that HL2 was not so great, since it won the "best game of the millenia" awards all over the place when it was out (and it was way over-hyped even at the time).