I cant really answer this question definitively, since I use my own customised skill tree, but I do find that my attempts to have combined arms combat/support ships have tended to end in failure, the support ships simply dont provide enough support to make up for the loss of a combat ship. A lot of this has to do with the fact that the hp/sec regen of a support ship does not match the dps/sec of an equivilant combat ship. Thus, your better off just going pure combat ships as, while your slightly less durable, your DPS will be much higher so you will likely be ending fights before durability becomes an issue.
Thus, the best trees would likely be Gunners or Pilots. Missiles have great burst damage, but once you blow through the munitions (and missile ships in star wolves have little ammunition capacity) your a sitting duck while a gunner can pretty much shoot until he is destroyed.
As for the best ships, in Star Wolves 3, the best ships are, by far, the Templar variants.
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