Where do you put your resources?
There is a saying in prepping/survivalism circles that if you prepare for any type of catastrophe, you prepare for none.
The flip-side of that, though, is that if you prepare for one type of catastrophe, it's one of the ones that you aren't ready for that is going to get you.
I've been reading some rather alarming things about the possibility of Yellowstone erupting - the park itself is situated in the caldera (that is - the mouth) of a mega-volcano. The potential is for so much damage that the world as we know it will be wiped out, to a possible global mass extinction... Sulfur compounds choking the air, sulfuric acid devastating plant and sea life, spewing enough dust into the air to freeze non-equatorial regions.
How can you prepare for that?
Apart from completely isolating yourself for decades in an artificial biosphere? Could you maintain the systems to keep everything functional?
I do see a future for vaults, although I think people are limited in their scope, and how they go about designing them - that's if they design them at all. Most of the time, they are re-using old missile silos, rather than starting from the bottom; they design around what they already have, rather than what is actually needed. Not that the basic principle isn't valid for emergencies, but if you are planning on something which can support people for periods longer than a week or two, then you need to be smart.