Hmmm, let's see
Here's the priority I tend to follow:
(1) Power-curve - two elements (a) how much power left over if running spd 31, (b) full alpha recharge speed maintained
(2) weaponry makeup of ship; weapon arcs if especially good; recharge rate of weapons
(3) shields
(4) turn-rate (when not flying Gorn)
(5) tractors, shuttle-bay launch rate, transporters, max marines held
I tend to fly ships have give you the most tactical options. You never know when you will have to change your attack/defense strategy in mid-mission.
Agave