Maybe a way to negate the whole problem with pirates and planet colonization (ie. needing to make pirates prioritise colonisation ships) is to give a planet a sort of residual atmospheric shield (or preparing the atmosphere to allow the modules to enter or to prepare the site of landing) that would need to be overcome by a frigate (maybe all frigates or maybe just siege frigates) with a 30 second countdown ability, or something like that, that would restrict a player from killing all the pillagers only and then colonizing and running away to do it again.

The advantages of this is that it allows the pirates to have a much more conventional AI prioritization, meaning that any planet needs a much more conventional strategy to be taken over with a typical fleet destroying all the pirates and then colonizing, instead of a colonization ship "hit and run" strategy where the pillagers are taken out along the way, allowing an empire to grow much faster then should be able.

The pirate AI could then focus on ships on a most destructive basis, only to be distracted by ships trying to prepare the landing site.

I know that this may not be the perfect answer, but it allows the AI a much better chance at defending it's planets.

Shaun