well as tobis partner, i dont think he ignored tobis powers. hes as perceptive or more so than konan. hed know the secret of his power and eventually land a hit on him with ST, CT, konan summon, cerberus summon. tobi has good chakra levels but he doesnt like to be up close and personal. thats a huge advantage. nagato can bombard him with multiple high level attacks. and if he summons konan, he can have her fill her paper clone with bombs and send it at tobi while nagato has him distracted.
tobis best hope is finding and genjutsuing the original nagato while nagatos busy attacking with 6 pains and summons.
i assume nagato has posession of the gedo? tobi may know a weakness in that thing. but he lacks any real jutsus so far. lets wait for 595.