From other games, simple target priority(target weakest/target strongest/target nearest) seems simple to implement and appealing.  The problem with allowing targeting is that it makes planetary invasion difficult. 

 In GalCiv II, I constructed very fast "Striker class" ships.  These had a minimal weapon, cargo hull, maximum sensors, massive engines for speed.  Their purpose was find and destroy all unarmed resources with priority to unguarded troop transports.  This (plus super fast transports to hit any planet without ships in orbit) allowed easy defeat of much stronger enemies.  (More expensive engines in Dark Avatar helped even the playing field by making this option less viable.)  The main defense against this strategy is incorporating troop transports into fleets with escorts. 

 If target priority is allowed, then a weak  attacker could always hit the unarmed transports first to prevent planetary invasion.  This would drastically tilt the game in the favor of defense and eliminate the whole point of an escorted transport.