I played 5 minutes, the first thing that happens to me, I spot an alien craft (please, change them, make then look like ufos, not starwars ships) and i send my stiletto after it. I can see it will engage it over the ocean, so I checked if there were any orders I could give, I found there were nothing I could do but watch it take it down and lose the ufo in the ocean. Pretty good hu?!.
Crafts should be handled just like in XCOM, they get there and you choose if and when to engage. So you can follow a ship.
You should be able to send any ship to a landing ufo zone, if the ufo takes off, you can engage it. You could also bomb it with a fighter, and have a chance to hit aliens, also break ship parts and even harm civilians