I always start by eliminating smaller ships first (playing as Imps) as once Corvettes and Frigates get behind your Destroyers it is a major pain in the woowoo to turn around and attack them.
This is why I prefer fleets of Victory Class ships to Imperial Class ships. Smaller and more agile.
EDIT: I've also found that, while playing as Rebels with Mon Cals, it's pointless to target shield generators as by the time you're close to them the ion cannons/y-wings have already knocked out their shields. This allows you to target more critical hardpoints like turbolasers or hangers.