Keep in mind, excess Rage is not 'wasted' due to Inner Rage--it is just translated into a temporary damage buff. Therefore Shield Specialization is a net DPS increase regardless of if you 'need' the Rage or not. (In fact, it's a bigger DPS increase if you don't need the Rage.)
Also, I would say Vigilance will be taken in most boss-oriented raiding specs simply due to its utility for providing higher Vengeance stacks when there is another tank around--either for off-tanking or to prevent drop-offs due to small periods of not being hit.
With the new structure, I would not at all be surprised if most tanks just grabbed Blood and Thunder in Tier 1 and skipped Incite. Honestly, Incite is not very great for Protection and was only really taken in the previous builds as a back-filler to min/max single-target DPS. If given the choice between Incite and Blood and Thunder specifically, I'm guessing most will take Blood and Thunder. (I have to say that I'm not a fan of the new Tier 1 structure, as it really restricts the choices we have in terms of our floating points...but that's another issue.)