Ryan, it was a rough day, no question. I read that Gil himself was upset, saying words to the effect that "it's not supposed to go like this."
The question, that I think you raised, is whether that harshness is part and parcel of the design/construction, or a temporary condition that will change naturally as the course grows in. From what I read it's the latter.
It says a lot to me that everyone I've read on GCA.com who's played the new course, really, really likes it.