Naruto gained more self control and learned more innovative ways to utilize the skills he had. Mainly in the field of his Shadow clones and his Rasengan. He possess better timing with his clones and a higher degree of deception. In part 2 he wasn't the idiot who snuck inside Haku's Ice mirrors or made a big flashy entrance. His taijutsu increased to a degree. Also, for those that people that talked about Naruto's control over the Kyuubi, Naruto did gain the ability to access the chakra and maintain a level of conscious control over it to a greater extent than he had previously. Naruto went berserk with a mere chakra leakage of the kyuubi when it was first demonstrated. When Jiraiya taught Naruto the summoning jutsu he taught Naruto how to rudimentarily access the chakra. In Part 2 Jiraiya stated Naruto could maintain a cloak of the Kyuubi chakra up to three tails without loosing his sanity and going off the deepend. Though I think this was false, I can't remember if he had attacked Kakashi by mistake within the cloaked form when they fought against Deidara. However, in overall growth upon his return, in comparison to his other two teammates, he progressed the least.
Naruto was still arguably stronger than Sakura in the beginning times of part 2, however, her progression was significantly more to the point, Naruto would have trouble with her as opposed to in part 1 where he could've, most likely, taken her down with the minimalist effort, had he wanted to. However, it is that feat that status in part 1 and the status in part 2 that makes her progression more potent. She became a medic comparable to Shizune who is renoun, and she gained the strength of Tsunade and better taijutsu. I personally believe her taijutsu took a jump forward however I still feel her only adept skill in tai is her evassive ability and strength. As far as technique, she's lower level than other prodominent taijutsu users and even Naruto now.
Sasuke's progression was lesser than Sakura's as well. Sasuke's always been the prodigy, really, the only showcase in advancement was his Chidori varrients, which can be compared to Naruto's Rasengan varrients as the only diff is the shape in which Sasuke manipulates the raiton chakra. Then his Sharingan naturally developed being an Uchiha, he became more adept in genjutsu. As well the snake techniques he had, though I don't remember seeing anything with his prowess in snakes until after defeating Orochimaru in his sick bed. However this didn't say anything to Sasuke's significant progression. His skill level progressed at the rate most would expect it too given his previous situation as a prodigy. His progressions were minor in overall comparison however it still kept him grades above Sakura and Sasuke.
The rest of the Konoha 11 though? Those mother ****ers just got a lil older and that's it.
The reason for Naruto's limited progression in the timeskip is probably because, his ascention to his peek point, which is what we're at now, is something people wanted to see. I mean they wanted to see a badass Naruto right off the back, but if too much was given then Naruto would've just been OP or far to skilled and any advancements wouldn't have been as significant in the plot progression. Half the story is about Naruto gaining some badassery. If Naruto had Sage Mode when he came back from his trip, how would that have looked for the plot. He could've found Sasuke himself, and forced him back to the village prior to him ever reaching Itachi and Naruto could've ****ed with him easier than he could've have with Mangekyou Sharingan. He'd had have more time to progress and learn to control the Kyuubi allowing him to probably defeat Pain hte moment he tried to come into Konoha. Then we'd be at where he was now, with mastery over the Kyuubi, before the War started and we're in a rute for like 200 manga chapters with him not progressing anywhere because he probably won't gain too much else before the series ends. Maybe something legendary, blah blah, Sage of 6 Paths legacy shit yada yada. However that's like the big finish so it has to go in the end otherwise it's not significant.
