I defiantly think there could've been better intergration, and having to use Google+ to comment is a mistake. But threaded replies is good, and not all over the place, but it does need work. And the poor implentation of this and the reacent settings on the video bar change are the only two things that bug me. I think Youtube has gotten a little better since Google got it. I like the description down there, it's cleaner.
I think the comment implantation will get better. And Google is pushing G+ to be sort of a internet ID, not sure how much I like that, but its kind of one log in, and I've been using it. People on G+ are nicer, and a few youtubers actually said g+ is great, minus this ofcourse.