I hope this doesn't come off as a bashing post as that isn't my intention.
My first gripe are the battles. They don't make sense - the battles shouldn't have been short. Edo Nagato was gone in I believe one or two chapters while a lot more stuff was going on. The Seven Kiri Swordsmen were out in a couple to.. Heck all but Edo Madara and Edo Itachi were gone in one or two. The war should have been on a larger scale with more people dying - seeing how fast the Edo Ninja died, I can't imagine how 40,000 Ninja died during this war and Zetsu didn't kill that much.. That wouldn't make sense.
I would have preferred longer more grandiose battle. They should encompass 5-6+ chapters depending on the importance of each character. Nagato deserved a lot more chapters than he got. Look at the Invasion of Pain. Kakashi got several chapters to fight Tendō.. This was a single front as well. This should have been the case during the war.
The second is the plot in general. Why is so much happening so fast? Kabuto died, Sasuke betrayed Tobi, Tobi was revealed to [not be Madara] be Obito, Naruto garnered Bijū Mode, Jūbi was summoned, Orochimaru was revived etc. This happened in two days.. Two! What kind of war is this?
From the tales of Jiraiya, Hiruzen, Hashirama etc. the wars lasted really long. This was because the war was on equal footings.. I will argue that it is on equal footings. Kishimoto is clearly rushing the manga.. Why? Publishers or something but it's clearly pulling down the plot. And what exactly are the ninja other than Rookie 9, Taka, Kakashi and Gai as well as the Edo Hokage even doing? Why don't they retreat as they're clearly not doing anything productive.retreat and regroup and launch an ambitious attack on the Jūbi or something. Not just stand and freak out when the Ten Tails attacks.
Next, Edo Tensei. This jutsu is ruined - okay, it shouldn't be so easy to use. It is the greatest technique ever. Only Banbūtso Sozo, Rinne Tensei, Kamui & Kotamatsukami can rival it. How in gods name was Kabuto able to control so many ninja and some of the most powerful ones at that? Why was Kabuto such a bad user of the jutsu as well - why didn't he restrict the emotions of more ninja? Why didn't he abuse Nagato more? In addition, imagine the war without Edo Tensei. More grande battles with Zetsu [actually war like] and Tobi would seem more menacing seeing he was confident that two ninja could solo the whole NV.
Now with Hashirama and others on the battlefield, it seems like the old-gen will save the new-gen and that shouldn't happen. That destroys one of the many morals taught in Part 1. And, why didn't Hiashi meet Neji? Like, was it that hard..
There are also many inconsistencies. Why did Hiruzen not give a sh*t when he heard Sasuke killed Danzō? This little boy that he ruined the life of another to save killed arguably his best friend. No emotion? How does that work...? Also, why did Sasuke change do fast? Insults the Sandaime in front of Kakashi, kills a Hokage then listens to them. Why? Because Itachi said I love you or something. He shouldn't have changed so quickly.. It's so unrealistic, even for Sasuke.
Now onto the deaths. Shikaku, Ao, Inoichi, Neji.. That's all I can think of, off the top of my head who died. We know at least a hundred shinobi who are quite important - why did only four who received no development die? Heck, Jiraiya, Hinata, Kakashi, Tsunade all died during the Invasion of Pain or appeared dead. In a one man fighting a country, more people died than three men, one with seven monsters, another with 100,000 of himself and another who controls 30+ other ninja. More people [Gai, Kirabi, Gokage] should or should have died.
That's my analysis.