I think Ghost Hound was a writing mess, really. It tried to portray itself as Higurashi as envisioned by Shirow Masamune and Production I.G. in the beginning, then went through an Evangelion-like super deep analysis of philosophical, mythological, psychological and moral concepts before giving us this weird, anti-climatic and not that satisfying ending.
Quite literally, the middle section of Ghost Hound after all the "I shat bricks!" moments ended was meant to shock the viewer. Miyako as Taro's sister, the would-be affair between the scientist and Masayuki's dad which evolved into Masayuki fucking with her, Makoto attempting to kill his mother and Taro's journey into the land of the dead.
The conspiracy plot was good, but felt out of place in this supernatural show. It would have been more appropriate in Higurashi. By the last episode, the show barely resembled what it originally started as.
I think Ghost Hound tried to be too many things, I.G. got too upity with Masamune's script thinking they could make a super hit anime, which ended up going all over the place and had to get cut four episodes short because people didn't know what was going on.