Single enemy ships never have a chance. You see which aircraft the enemy is tracking. Send that one off in one direction and come around behind with your other aircraft. It works every time and after taking out an arbitrary number of ships this way it doesn't feel very interesting any more.
Obviously you have the upper hand in a 2 on 1 battle. It is just that the single enemy ships don't seem worth it to have the whole air battle radar thing popup, it doesn't really contribute anything to the game experience. Radar pops up, oh single ship again, click one fighter one direction, click one fighter the opposite to flank, win. Currently the single enemy battles don't add anything to the experience for me.
Now the corvette ships with multiple fighters, I haven't had any luck besting those with only 2 fighters.