You're absolutely right, he was very important...in part one. Part two, if you haven't noticed, has taken major shifts away from part one. Notice the reduction in every character except for Naruto/Kakashi/Obito's time spent in focus? That's why. The series is nearing closer to the end, so the time has come for the main characters to start taking the stage. It doesn't matter if characters aren't 'fodder' at this point. If they don't have Magnekyo Sharingan, A tailed beast, or some other over powered ability, they're going to slide out of focus. It's not like Shikamaru has gotten more development recently than anyone like A or Darui. Or Tsunade, for that matter. They're all being phased out for the climax.
And as for Kidomaru, that's still fighting genius. Shikamaru has the genius to lead, which is different than what Neji has. There's more than one way to be intelligent, and right now, if you aren't grossly over powered, Kishi favors the latter.
