I got a lot, I will do as I remember in a few part. ( I still really really love Naruto ).
- Obito not going himself capture all the jinchuriki.
- The way Deidera, on of the master card of the war, was taken out. At this point everyone know that Deidera fear Raiton.
If Deidera had been protected by let say Hanzou the Salamander and the 3 Raikage, he could have spammed big explosions without fear and single-handely take out most of the alliance.
- Orochimaru beginning to fight against Sarutobi only after the Two Hokages was sealed. He could have helped the Two Hokage with Kusanagi and Snakes and easily won that fight. Why was he waiting ?
- White Zetsus. Who wants to see people foghting white zetsus ? Naruto is really rich in good designs and they have to fight white Zetsus ?
- The number of Chunin and Jounin with a Chunin exam that Hard with only like 1-3 passing the test each year for each village.
Where did they find those tens of thousands shinobis ?
200 - 300 Chunins and Jounins by Villages is more believable and largely enough. 1200 Shinobis on the war and that's good.
I don't care Ohniki said Minato took 1000 ninjas by himself ( that's too big by the way ), thousands of Shinobis by village makes no sense.
- Sending Naruto, Kyubi Genin, fighting Gaara Ichibi genin ?
Naruto knowing his value should have been greatly protected and properly trained. And you don't send an impredictable genin fighting Suna master card. Gaara killed jounins without trouble.
- The way the village treated Naruto when he was young when he was the son of heroes and the 3 of them were sacrifice for the stability in the village.
- If you have so many shinobis by country, how do you explain that for taking back, Sasuke, the only Uchiha from Orochimaru, a very dangerous Shniobi you send a team of a Chunin and 4 genin ? Tsunade ahould have gone too.
Plus, take some guard. But Orochimaru is already getting Sasuke, you really really want to give him Kyubi kid and Hyuga genius ?
( - Orochimaru could have taken Neji as new body. The guy still has okay eyes and good corpse. Okay not on Kimimaro level but like in stock ).
- This is very personal but the way shinobis foghted during the war....
You are NINJAS. You can jump everywhere and fight 3D. Why are you all amassed in group waiting to be slaughtered all together by big nijutsus and explosions ?
Asuman and 3 Chunin could defeat 1 Akatsuki.
Kakashi and 3 other Jounin level, Naruto, Sakura and Chiyo kind if defeated 30% Itachi.
It is all he should have been. Team of 7-8 persons fighting big names during the war. The tens of thousands just totally annihilate the hype of strong shinobis.
8 NOT MAIN CHARACTER ( 8 good design jounin ? ) persons against each one of the Akatsuki waitng for HERO to save them. Okay I believe.
Madara and Hashirama are special cases.
- Madara and Hashirama were too strong, Pain or Obito as peak strenght were good enough.
- Juubi was not really interesting.
- Sarutobi not losing his cool and absolutely muder Orochimaru when discovering his awful deeds.