I would change many things
1. Produce different teams (war team) as separate but interwoven story lines instead of having just one continuous story line that jumped around from battlefield to another. This way one could spend more time developing each one individually.
2. I would have spent much more time on the war arc and developed much more abilities of other nations and wrote in many other powerful characters from each nation
3.Explored in-depth the various Edo's power's of past snobi, like Hanzo
4.Would have started killing characters that should have died ages ago, like kiba (attempting suicide), and have other snobi replace them
5. Have other character have some sort of past wounds, like Neji (poor heart), Rock lee (muscles tear easily), Naruto damaged chakara network in his hands, Sasuke (adverse side effects from chemical enhancements from Oro)
6. Explored and made each Jinkuri(sp) have unique traits and abilities in addition to having there own abilities as a ninja
7. Had some really awesome battles such as Sungetsu vs the 2nd Mizukage.
8. Last but not lest I would give some characters much needed development/ advancement. Such as tenten gaining Madara's war fan, Obito's sealing spikes, and the 1st Hokage's Forbidden scroll with her own summoning seal placed upon it. Bee loosing most of the 8 tails and gaining the Sot6P items. to compensate his unique fighting/ raping style. Or even having Henata developing the gentle fist medium range fighting style and "evolving"/ finding the stage of the Beykugan.