Plot. The whole reason why he slowed down was plot. Kishi gave him incredible speed which allowed him to be faster than V2 Ay. But then if he kept using that speed he would have simply blitzkrieg'd the entire Zetsu force, the Edo Army, Edo Madara and Obito, which story and entertainment wise would have sucked.
In DBZ happens the same with Goku's ability to instantaneously teleport anywhere. In one occasion he used it dozens of times in a row, virtually hitting his opponent from all angles at the same time. This could have been used against every opponent from thereafter, but it wouldn't make for a good show.
The same is true to Madara's and Obito's Rinnegan. Having Hashirama's DNA they could literally spam their Rinnegan techniques to full extent. Obito could have certainly do this against Kakashi, using Preta Path or even Deva Path. However if they would do that they would simply rape every-single character on the opposed side. Making the war a very dull Arc.
So in sum Kishi had to do what every author needs to do in order for the story to gain, temporarily forget what your characters can do. You may call it plot hole, I'd rather call it simply plot.
