I'm basically reposting this from the other day since I'm going to say the exact same thing, albeit with modifications to make it specific to this thread, which should really be in the "vs. threads" section, not the manga section.
I think Shikamaru's shadow bind is only an issue for Tobi when he's tangible like so many other jutsu in the Narutoverse. In the example you gave, I believe he was becoming tangible in order to teleport the Amber Pot with the KinGin brothers' Kyuubi chakra sealed inside, so he likely could've just phased out (i.e. intangible, thus what does the shadow bind?), killed Shikamaru, rematerialized, and then teleported away with the Amber Pot. However, he already had Gedo Mazo there, so he used Gedo Mazo, which when attacking Shikamaru, broke Shikamaru's hand seal and the corresponding shadow bind, thus freeing Tobi.
As well,
due to his [Shikamaru's] incredible intelligence Tobi was hoping to kill him with Gedo Mazo, as he felt he was too smart to allow to live given he was for the alliance.
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Notice the panel in the middle left that highlights Tobi hand grabbing the Amber pot, indicating that he's taking hold of it for teleportation and thus tangible before Shikamaru's shadow bind connects.
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Next page has a nice aerial view.
Shikamaru has ridiculously low chakra levels too, see his Chuunin finals exam vs. Temari. He would be dead for so many reasons if he fought Tobi, it's actually amusing to think about it, lol. For example, Tobi could drink ninja lemonade while he has Gedo Mazo chase Shikamaru until he runs out of chakra, lol.
In summary, aside from pure intellect...
Shikamaru < Tobi, albeit Tobi could be ugly as hell, so I'll reserve judgement on that for now with the whole mask thing being on.
Peace
