Simply put.

What happened to his Mangekyou Sharingan? What happened to this beast that took down Kiri's ANBU with neg-diff? What happened to his mokuton?!:

Obito was basically handicapped by plot during that fight. His chakra reserves were being drained by controlling Kurama , he didn't use his Mangekyou Sharingan, he didn't display mokuton (that kamui-mokuton combo was awesome), and where was Zetsu?!

It can even be said that Konan gave Obito a harder time than Minato did, as Obito had another sharingan eye at that point, and Konan forced him to use izanagi to save himself. And that was an older, much more experienced Obito.