You're right about her large base but Biden's low vote total from 2008 isn't a good guide since he has a much higher profile as Vice President. For instance, it's possible black voters would be behind Biden in 2016 as Obama's closest ally.
Biden's current job approvals and profile as Vice President suggest that a national base for him has not (yet) materialized. No base materialized in 2008 either. Perhaps he can find a way to address this, but frankly I am skeptical. Clinton has a large national constituency which is semi-independent from President Obama's. That's a big advantage that Biden lacks.
It IS an interesting question, what would Obama do if both Biden and Clinton jumped into the 2016 Dem primary? Probably stay neutral is my guess, although one never knows what is going on behind the scenes.