Well since mostly no one is giving a serious answer I might give one.
I love the way Kishimoto showed maturity factor in part 2. In part 1 they were mainly 12-13 years of age,and so the theme,their thoughts,etc. was like that suited for 13 years kids. But you can find the mature stuffs even in part 1 from the mature characters.
In part 2 all of them became 16 around and so did the theme. They just didn't grew in size but in every sense. Kishimoto changed the entire theme of manga,showed more realistic things that he mentioned as "It doesn't exists" in part 1 as those were the thoughts of naive 13 years old kids.
The theme of sadness,bond,friendship,loneliness,reality,illusion,darkness,love,war,peace,hatred,etc. are the most touching things. Very few mangas cover all these themes into one. Also the fact that no matter how powerful one is or gets,there is always a use of strategy. Power alone can definitely destroy things,if it's enough,but strategy alone can't defeat opponents. One needs a skill to see through that strategy till the end,and this is something that is not understood by bashers.
The philosophy,ideology,creativeness,plot,everything is superb. The inspiration from various mythologies makes me feel more close to it on spiritual level. The fact that every character is multidimensional like the real humans are. Villains just don't kill for the sake of killing,mostly. The uniqueness that is TNJ,the thing that tells us that one can solve things by talking each other,if one tries. And in the same time it also teaches that one needs action as well to make other understand that he is right.
There is a lot and lot more than I can list here but as for now I guess that's it.