Planet wide escalation increases over time (shown under your health in the top left). This increases overall difficulty of subsequent waves, in terms of enemy spawns, objective requirements and some other things. Escalation also affects some bosses and chest prices, generally you want it to not massively outpace your wave count. 100% per zone is a considered a low escalation run.
Viewing post in Drawback of staying longer?
Ah, for some reason I didn't notice it increased over time, though it only went up per wave and with some effects. Makes sense.
One more thing, what exactly counts as "ace a whole zone" for the ship unlock? I thought I had a run where I had "flawless" on every wave in first zone (I assume you get that for not taking hp damage) but it didn't unlock. Of course I might have missed something, but it's also possible I'm misunderstanding the condition.