If I remember correctly VM is sensor and SNB is deflector based so how can they have a shared cool down?
SNB does not have a great duration either so what is the problem?
Yep, Viral Matrix is Sensor Probes and Sub-Nucleonic Beam is Deflector Dish. So, I don't think they should share a cool down timer (IMO). I can't speak for the PvP side of things since I haven't done any in this game yet.
I would rather see CC in general if it has to stay not last more than five or ten seconds. The phaser subsystem proc for example doesn't last long and has a very low chance like the others. It would also be more rewarding if you could only slot one rank of a skill to broaden things out somewhat. If I can only use one engi team and one science team rank that makes more people think what version they want and how to fill out the rest.
It would be nice if the rank three versions that can be taught help in being a deciding factor for each captain type.