Based on that analysis, MJ, it seems like it makes sense to gun for the shuttle first. You want to make Palpatine spend his ability defensively on the shuttle, which is the least efficient way possible. The fewer times you give him a chance to give an HP to an ace, the better.
It depends on the matchup. If you are flying a swarm, then that probably makes sense, because you can burn it down in 1-2 turns. If you are flying BroBots, then going after the shuttle is almost certain suicide. One of your IGs is likely to be dead before the Shuttle is.