While a vault would be a little more organized than a collection of chests or an area staked out around a teleporter pad (etc), I like the freedom of being able to arrange stuff the way I want. Of course a large vault with a variety of containers could allow just as much flexibility.
Some people have also requested weapon stands, etc to display their collection in their house/base.
As for the security implied by a vault, I agree it would be more realistic to have to lock up your valuables, but in practice it is a pain if stuff starts disappearing if you leave it on the ground too long (etc).
In general, I don't really like time limits. It may make sense for some quests, though, as long as the limits are reasonable.
