If your medium ship with very little weaponry but lots of defence is being favoured as a target it could be because it has a fleet support module. As a 'command ship' it gets punted to the top of the targeting list.

One problem with this tactic is that eventually the AI will come up with ships that dish out so much damage that your defence will be overwhelmed. Also, although surviving many battles will gain your fleet some experience and hitpoints, the one that gets targeted first is the command ship. You may want to rotate out some of your experienced ships and upgrade them to ships which have weapons and defence, since the extra hitpoints will make them worth investing some credits in.

I go with the good ethic choice and hence defences are quite important to my ship design.

Personally i've found you want your largest ship targeted because it has the most HP and greatest potential for defences. Like Marvin Kosh said the AI may come up with the critical mass of offensive firepower to bleed through your defence. Its not pretty when that happens.

The way to ensure your largest ship is targeted, barring command mods, is to make it the most dangerous while not outstripping its sister ships by a large margin in defensive capability - thats a quick way to lose the supporting ships as the AI will retarget.

This may not be to your playstyle, but if you do favour defensive techs then try to maintain at least 2 defensive lines at once. When ships have considerable defensive values in all 3 defensive types not only are you safe from multiple weapon types but the "off" defenses still give you a roll.

Even only at the square root value the additional rolls seem to work wonders at soaking up anything that would have otherwise gotten through your primary defence type.

At the end of the day it pretty much comes down to experience at being able to judge if your fleet is still invulnerable to the enemy - I'd suggest experimenting and don't get discouraged if you make a bad call.

I'm also not sure how effective defences are without additional %defence and good bonus so if you play without these factors take what i said with a large grain of salt.

There's no special targeting preference--ships are simply ranked by the formula Attack power / (HP+Defenses), with the highest result being shot at first. The fleet boost modules do boost a ship's priority in the calculation, though the specific amounts have not been disclosed.

I have found that unless you get into the REALLY late game its very easy to destroy the computer to the point where it almost feels like armor stacking is an exploit. I have used one ship with just 12 armor and 2 (yes 2) damage to take out an entire mid game armada. The computer, predictably, ignores armor until late in the game and just busts out 6 damage of one type ships with at most 1 or 2 in defense if you want long enough.

This means that even in a long one ship vs fleet fight your two attack ship will take down 4 or 5 enemy ships while taking at most one or two points of damage. While 12 armor may sound like a lot, if the enemy goes for beam weapons or missles 12 defense is achievable in just 20 slot points just a few techs into the respective trees. In 30 weeks of research you can make unkillable ships which will destroy hundreds of the enemies ships for a fraction of the cost. The only problem is letting the AI get all the way down to things like Nightmare missiles which best all defenses unless you're going to make huge full miniaturization high defense ships with 200+ defense, and even then randomness and fleet sizes will probably do in any and all high defense strategies. At that point it becomes a question of other strategies, but anywhere from the mid to early late game it is more then possible to have one ship become stronger then all the enemies ships combined through defense stacking. As a final note defense stacking works best with laser V since you only need 5 units to place a laser leaving plenty of room for defense stacking even on a tiny or small ship.

To be honest I wish this could be fixed somehow, I know technically I could just not "exploit" this hole in the AI, but it really makes wars just way way too easy. Ever since finding it I have not lost a single game nor come even close even on painful or above settings. I was able to make 60 credit tiny ships that bested the enemies medium ships thanks to defense stacking in an unexpected early game war, its just patently unfair how badly defense stacking destroys the AI at every turn.