Fighters aren't very good against frigs, so they go after strikecraft instead.  If you want to them to go after the other guys' frigs then get bombers instead of fighters.  But then don't complain when their fighters kill all your bombers.

Maybe adaptive targeting could be nice: If a player always selects LR frigs for their fighters, eventually the autotargeting would start to prioritize the LRFs.

Or you could put some under-the-hood settings for this in a config file. Player that like to tinker or get really annoyed could just do a few settings in notepad.