another issue with Loki letting Thor rule and pulling the strings/advising him, and I suspect that it will be expanded on in Thor 2, is that when Loki tries to do something or give advice to Thor early on in Thor there are several instances where he pretty much says, "shut up Loki'" and so I can certainly see where Loki is not feeling like his voice is heard or that his opinion is worth anything to Thor and possibly his whole family and "friends"
examples, the exchange with Heimdall before going to Jotunheim (the way he say "let me handle this" and then the look on Loki's face when brother says "Enough!")
"Know your place brother!" on Jotunheim when Loki tries to get Thor to back off for all their sakes.
I think there was one or two other little things which I am blanking on, moments when you can really see Loki in Thor's shadow. And again I do think will be addressed in Thor2 as one of the "major bones of their conflict" as Hemsworth put it. but the point is little brother is really trying to make good use of himself and big brother is like "shut up dumbass, let me handle this."