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 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.
I don't think Shikamaru is necessarily the key to Tobi's demise because that screws with the whole destined child plot for Naruto if you think about it in a way unless Kishi writes it such that all of Naruto's friends play key roles along with Naruto, which would be kind of cool. Thus, I think it would be an all or none thing (i.e. all his friends or none of his friends, which harkens back to Itachi's comments about those who become Hokage), not just one or two friends like Shikamaru unless the contributions are minor. Further, we were recently shown all of Naruto's friends being sent to reinforce him by Shukaku via Inoichi (who had a freakin' cocaine nose bleed from the transmission, lol

).
Thus, you may very well be on to Shikamaru's role, but it's not a terribly surprising one, given it's what he's done all series long in groups or solo (Hidan), genius with the shadow bind Nara clan techniques. Further, Tobi likely has an easy counter to this (phasing) since he only has to be tangible to attack and teleport, so it's really about Shikamaru's genius (i.e. learning the 5 minute limit) more than anything that makes him important. Tobi wasn't disappointed to have to kill him because of Shikamaru's jutsu but because of his brains.
Peace