Question... does the bloodline templates work like the racial templates. Like I need at least 3 ranks in Byakkugan by level 6 in order to gain all the skills that come with Being of the Bloodline without having to worry about putting in more ranks?
Well, if you take 3 levels in Byakugan then no, you wouldn't have to take anymore. But you'd also have a CL of 3 when everyone else probably has 5 or 6, which I can tell you from experience, isn't very fun.
The only difference, classes-wise, between human and non-human shinobi is that humans get an extra skill. If you play as a non-human shinobi you get one less skill than is listed for each class. I think that answers your question, but I might have misunderstood.