I don't know if marioflag was talking about my post in another thread, but I actually asked that question and said that it was my impression the enemy fleet went for the ship with highest hitpoints. But I'm at work now and cannot check. It is also possible that it was due to the beta and it may have been changed since (which I asked too).
Now that being said,
The example I mentionned was, let's have a fleet o 3 ships one smal and 2 mediums. The small one has a lot of experience, and its hitpoints reach 45-48. The 2 medium ships are brand new an therefore with its base hitpoints only (I don't remember, but something like 22-don't remember exactly).
The medium ships had more defenses and attack than the small one, but less hitpoints.
I had the distinct impression that the only ship fired at by the enely defending fleet was the small one.
On the other hand, I might be wrong, and another element interfered: I have a military starbase that adds defense and attack to the ships, so maybe with the bonuses, the small ship ratios seemed more threatening.
I don't remember exactly how the battle went because I thought about it later, womdering if I could build a fleet of a medium ship with lots of defenses to attract enemy fire and fighters with only weapons and no defenses to attack.
I wanted confirmation of this from someone more familiar with galciv2 than I am