One of the major reasons NIST selected Keccak to be an alternative SHA standard is because it's a very different kind of hash function than SHA-2.

What this means for Nexus is that it will have different weaknesses than Bitcoin does.  A successful attack against SHA-2 will be very, very bad for Bitcoin, but won't break Nexus.  A successful attack against SHA-3 will be bad for Nexus, but probably not for Bitcoin.  It's good to have currencies that don't depend critically on the same cryptography.

http://stackoverflow.com/questions/14356526/whats-the-difference-between-the-hash-algorithms-sha-2-and-sha-3