Lol Jiraiya spent only a few more months training those three scamps with no prior ninja training then he did with Naruto and they all learned more interesting techniques than Naruto has displayed since he came back. Maybe the Rasengan+Kyubii control are just so great that there's no point in learning more but still, I'm much more impressed with those three's progress than anything Naruto has accomplished other than learning Rasengan.

As to the Tobi-Pein thing, maybe Tobi isn't fully in charge like we thought but he's on equal terms with Pein and just has a bad attitude. If Pein is a fairly tolerant guy then he wouldn't be bothered by Tobi talking shit to him and they could be working as partners for whatever nefarious goal they might have.