Everyone was using Yamato. Other than attempting to put bijuu's & jinchuurikis under control, Kakashi was the only person that didn't see him as an asset until Naruto came along(and Gai too)
Kabuto captured him... Bigger things were happening at the moment. He was trapped in a statue, white Zetsu came and took his body. Hopefully he can use that technique(statue) on his own now. Can you say power upgrade.