I hate a few things. I shall break them up into a few points.
1: The lack of missions in Part 1, and how some of the things we learned were either retconned, or never touched upon again. I personally think that we shoulda learned more and met or further introduced to the other villages in the first part.
2: The Akatsuki died off a bit too earlier, and the other Jin shoulda been shown fighting them. More epic battles and such in the manga, but with a reason for being there and so when the Edo Jin arrive we can somewhat like them.
3: Too much focus on the Senju-Uchiha Clans. I can understand if you put more attention into them later in the second half, but really. The Hyuuga, Nara, Aburame, ETC coulda got more stuff in.
4: Otogakure should have been an actual village with a hidden research center for Orochimaru. The Sound Five shoulda stayed.
5: KCM/BM. I dunno, I think Naruto got them too early. I think Sage mode shoulda been used much longer. They also are too OP.
6: The War itself was bland and tasteless, few battles were touched upon. But, cuddo's to the Darui versus Gold and Silver Bro's. THAT was cool.
7: The Rinnegan is a bit over used. I personally think only Nagato should of had it, but if it must have another wielder it shoulda been Obito, having stolen it. I dislike the whole "Oh, hey. Madara transplanted the eyes and even as a kid Nagato had such huge reserves to always have them active. When a Jounin like Kakashi got worn out by using his sharingan in a single battle!"