I know personally from some of my friends that they stated Part 1 was superior to part 2 but that's not what this topic is going to be about...I despise flame wars. BAH!
Anyhow, do you feel that certain things that were introduced in part 2 would have felt much adaptable rather than ass-pulls if they were revealed in part 1?. For example...
-The introduction of Rikudou Sennin and the Rinnegan: We were only introduced to these important factors to the story shortly after The Akatsuki Leader ala Pain aka Nagato was introduced. Do you feel that if they had some told us the viewers back in part 1 about such an important figure that it could feel more in depth. I don't have so much a problem with the Rinnegan being introduced so late into the series though. But If you remember in the earlier chapters in part 2 when the AL was introduced as a silhouette, he didn't have the Rinnegan, some people speculated that he was an Uchiha, maybe Shisui at the time or even the 4th Hokage. IMO Kishi still hadn't thought of the ocular jutsu at that time.
I personally enjoyed how the Akatsuki leader was portrayed after his reveal but his personality was nothing like I thought of him to be ala Makoto Shishio from Kenshin before his reveal.
-The Senju/Uchiha Connection: Throughout part 1 we knew that the Uchiha clan was a once proud clan before the massacre and were held on the same level as the Huygga Clan. But their was never any mention about their relationship with The Senju. And while his appearance was very brief until this current arc, we really didn't know much about the first and 2nd Hokage. Hell we didn't even know their names until shortly after Itachi's death. I feel that it should have been introduced in part one at some point to help flesh it out more in part 2.
-Danzou: He should have been introduced as well in part 1, at least after the thirds death. He was a great character for his schemes and goals could have made his connection in part 2 even more dramatic with his position in the foundation.
-Naruto's parents: I don't mind that the 4th is Naruto's dad but they way they kept it so secret in part 1 and revealed it in part 2 was awful. For example the 3rd knew who his parents where but in part 1 he stated at one point that the 4th sealed the Nine tails in the boy to protect the kid, he didn't say it was his son and when itachi stated he was after the 4th's legacy...Why say that? Can't you just say his son? This could have been handled much better as well.
-The "Jinchuuriki": The term was never used in part 1 but as soon as part 2 was introduced we heard the term from Deidara and Sasori. At first I thought it was something only the Akatsuki knew about but it turns out later that everyone knew what it was. Back in part one, everyone simply called Naruto the Nine tails like Orochimaru did. Also they never gave the connection about Naruto and Garra during their encounters at the exam. It would have been more fleshed out if they did in part 1, letting us know that their are other tailed beasts instead of having Chiyo from part 2 explain that which felt rushed.
Any other suggestions are welcome!