I agree with the OP, I think combat is too short as well and for quite some time now.
And I am not factoring player skill in this because it is a variable that cannot be defined, each player plays in a different way we are not automatons we are people, so what has to be evaluated is the raw impersonal data, which right now shows that combat is simply too short.
Make the system in its core more long lasting, and then this will fluctuate based on player skill some will reduce it some will make it longer, but as the OP evaluates, on average it should be longer than it is right now.
If shields had meaning it would prolong the fights somewhat. I think the problem is if cruisers get more shielding then what do you do with the already easy PVE side of the game. It's a damned if you do damned if you don't issue. This would really require a monster balance pass over to increase fight duration in PVP without screwing PVE.
Does it actually matter how PvE is balanced? As long as I can complete a PvE encounter, it doesn't really matter to me how weak or powerful my ship or powers might be in that encounter.
Balance matters in PvP because once you are losing, you will tend to continue losing. Usually until you figure out the same OP power set, build, or gear that everyone else is using.