Don't forget that, while the Manga doesn't translate motion very well, Naruto is supposed to be stupid fast now. As in, one of the fastest ninja alive, period. There's a chance that Tobi just didn't have enough time to activate the Rinnegan. Also, he hasn't had it that long? Maybe he's not that good with it afterall. Maybe he isn't even that good of a fighter; I mean, think about it. All we've seen him do is use others to do his fighting, and phase out when he gets attacked. I really don't think he's on the level without his space-time ninjutsu.