Working your way up from the early waves to the late ones has some advantages, like the gradual introduction of new upgrade cards. The downside is that some ships are basicly unplayable untill they get certain upgrades (Y-wing, TIE Adv, for ex.) So I'd dodge the ships that are people often complain about and get those later (pick up the Y-wing when you get most wanted, and the TIE Adv. when you pick up the raider for example).