As far as I know Kubo Formalism implies that conductance is proportional to the noise (fluctuation-dissipation theorem) in the conductor... So it really applies to very small bias scenarios.
NEGF (Keldysh), on the other hand is NOT limited to linear response, it can deal with high-bias scenarios INCLUDING the perturbative effects of contacts (broadening, spilling states into the channel)..
A good example is the analysis of a MOSFET where linear response is not the relevant mode of operation and the only meaningful analysis is the high-bias response. It can be fairly easily done by NEGF, say, for a ballistic device, but Kubo would not even be applicable.
Also in tunneling problems; the contact can play a major role so it must be somehow included in the model (something that cannot be done by Kubo), although no one really knows the exact shape of a 'real' contact, a phenomenological model is always possible...
So if your work is somehow connected with real experiments and devices; there are a number of reasons where NEGF is superior over Kubo; considering its power and its endearing simplicity...