Board Thread:Versus Debates/@comment-31171723-20170128170340/@comment-3965545-20170208171737

Itachi knew what Madara was in his prime (EMS), not what he was as his "shell" aka Tobi he only knew that Tobi had Kamui. So he may have simply thought that Tobi was a weakened shell of the real Madara hence can't use his other techs.