The things I've noticed with ships:
1.) A high level / power tie fighter is almost necessary. Mine always goes first and instead of using his basic, I use his special - it's a guranteed foresight and helps keep him alive a little longer.
2.) Take out Plo first, then JC, then Ahsoka otherwise you'll be chasing a taunt through the whole match.
3.) If you can keep taking ships out, you'll force the AI opponent to use his reinforcements instead of it's specials.
4.) Home One squads are so much easier to take down than Endurance squads - at least in my experience.