This is actually to the Bad Robot people's advantage, because Abrams is directing and Lindelof, Kurtzman, and Orci are producing
I don't know. As noted earlier, I think STID could've used someone outside of that group to pop the bubble of how clever they were being with reference A, B, and C and to pay attention to plotholes.
A careful director or producer can catch these things in the process of crafting a movie, and in this case, I think it's simply the writers weren't held on any leash and Abrams isn't really the sort who cares about details and tends to care more about the flash than substance. That is things like pacing and performances, which in itself aren't bad, but are not a good way to rein in writers who might need some nudging in a different direction.
There's gotta be a mid-point between using writers as disposable stenographers and giving them carte blanche.