The way I see it, the Time Vault combo only works in a BU-based deck, because you need cards that allow you to hunt through your library for the combo pieces. Given that such cards are too powerful to begin with and arguably distastefully homogenize much of the vintage metagame, I feel a good way to answer Time Vault is to print cards that hate on the card-drawing and tutoring mechanics, to the same extent that Leyline of the Void and Planar Void hate on dredge.
The only such usable hate cards I can think of that do this currently are Chains of Mephistopheles (card-drawing hate) and Aven Mindcensor (tutoring hate). There is room for much more creative alternatives.
I think the printing of such cards will help answer the Time Vault (read: black-blue) problem. It won't make the strategy go extinct, just like no amount of Ichorid-hate has made the Ichorid deck go extinct. But forcing card-drawing/tutoring based decks to run anti-hate will make them more fragile and thus diversify the metagame.
While modifying the B/R list or adding errata can have violent, unforeseeable consequences, printing slightly better versions of Chains of Mephistopheles and Aven Mindcensor should allow for a more careful, controlled shift of the metagame with minimal disruption to the secondary market.
Finally, since hating on card-drawing and tutoring has a theme of nature and justice, it would most likely belong in green or white - colors which could use greater relevance in the vintage metagame.
I've posted some examples of what such hate cards might look like in separate threads:
http://www.themanadrain.com/index.php?topic=39560.0http://www.themanadrain.com/index.php?topic=39555.0
