Rarely is it effective (or even possible) to build ships designed to withstand everything your opponent may send against you. Something has to die first, and as the Supreme Space Admiral, it can often be to your benefit to decide what that is.
When there are two or more targets presented to a gunner, the gunner has a choice to make on what to shoot at. Your job is to make that choice as wrong as possible. This is increasingly relevant against longer range weaponry as more range presents more targets. When armor fails and shields collapse, your last refuge is deception.
There are four main weapons to deflating the efficiency of the enemy fleet:
Overkill is anything related to redundancy. Twenty cruisers firing five missiles each at a single frigate is great fun, but it is not usually the most efficient use of launchers. An ion cannon firing at unshielded craft over a shielded one is a more subtle example - attacking unshielded targets could be done by beam weapons instead, temporarily wasting the anti-shield potential of the ion cannon. Attacking unarmed ships over armed ones can also fall in this category.
Incoherency is the opposite of Overkill - fire spread out to the point of ineffectiveness. Many defenses in the game have a time based component, namely recharge or repair rates. The longer a shield or repair module is allowed to stay up, the longer it actively works against your fire. Spreading fire out incoherently often results in shield recharge extending, matching, or even outpacing weapons fire.
Inefficiency is a weapon-specific concern. Faster or smaller targets are harder to hit and result in more waste for various weapons. The gunner AI appears inherently aware of this and will pick easier targets to hit... provided you haven't ordered them otherwise.
Immunity is inefficiency taken to the extreme. Fighters faster than weapon tracking, scrambler defenses, or armored/shielded targets can sometimes be partially or completely immune to a weapon for all practical purposes. Gunners are also supposedly aware of this, they will de-prioritize anything they can't hit or penetrate after a few attempts in favor of something else.
Vulture orders causes gunners to prefer targets with damaged hulls. Vulture fleets can be spotted by their unerring and annoying tendency to immediately pick up on even slightly damaged targets. Often, after the destruction of the first ship, they will move on to the neighboring ship (that got damaged in the blast) since it logically has the next lowest health. If you'd rather avoid being focused down in this manner, armor plates can be used as an blast absorption barrier to mask hull damage.
Obviously this order set can cause a fair degree of overkill, but in the odd case of ships taking splash damage from each other or from fighters, it can also result in beam weapons being attracted to shielded (and immune) targets.
Cooperative orders cause gunners to prefer targets being attacked by other gunners, the peer-pressure of group orders. Cooperative fleets can be spotted by their tendency to attack only one or two targets out of an approaching line, sometimes after some initial shuffling. Invariably the first chosen target will be the first target to come in range. Afterward the fleet tends to cooperate on targets chosen by other factors.
This order set, like Vulture, results in a large degree of overkill, although at times can be more inefficient. It's a bit better now that we can delete 'attack fighters' orders, but you will still find units firing on completely inappropriate targets just because "everyone else is doing it".
Note that target painters are a de facto cooperative order. Painted targets are considered an 'easy hit' and will get priority, provided the gunner has an order to attack that target.
Rescuer orders are the complete opposite of the first two, prioritizing actively-firing enemy targets. This can at times be extremely desirable behavior considering how little damage it actually takes to significantly or completely cut the offensive power of enemy targets. Healthy, firing ships also tend to have healthy shields, so this order can be useful to direct shieldbreakers.
Unfortunately, rescuer also results in a hilarious amount of incoherency when presented with a large number of targets at once, causing gunners to rapidly flip targets each shot. Useful for spread-EMPs, for short ranged weapons that will be presented with only a small number of targets, or against non-regenerating enemies like fighters.
Retaliate: A selfish version of Rescuer, only acting on units firing on itself.
Percentile Craft Attack - e.g. "Attack frigates 50%, Attack cruisers 75%" are a modifier on the ease of hitting a target. A gunner with equal 50% attack frigates / 50% attack cruisers will preferentially attack cruisers, because most cruisers are easier to hit than frigates. Inequality in these orders can therefore introduce inefficiency as far as raw DPS is concerned - low tracking weapons firing at fast targets in particular.
This is also the only known order of the above that influences driving behavior. The next driving target selected has some relationship to the percentage.
Now that we know the thought process of gratuitous gunners a little better, let's see if we can't gather some terminology on how we can use that to our advantage to buy precious seconds.
The first few targets seen by the enemy are obviously going to be shot at. At worse, they'll be the subject of cooperative orders from the entire enemy fleet. Don't make it your flagship. The trailblazer will be blazing alright, but probably not in the way the crew had in mind. Consider putting budget armaments on your forward ships and try to keep them lightweight - armor is just expensive and isn't going to stop the pain train that is headed their way.
So the trailblazer went down and all the unpopular crew members with it. Who's next? Big Brother is, that's who. When faced with two targets going the same speed (your ships match speeds, right?) the bigger one is the easier one to hit, so gunners are naturally going to prefer that. This is a surprisingly useful tool in fleet design, as it gives you the ability to roughly determine what types of units die last, at the expense of allowing the first units to die easier. For example, I've taken to making my AA frigates larger than my DPS frigates, so my AA frigates can better serve as later cannon fodder in the case of weak air resistance.
Note that this doesn't have to be the biggest ship in your arsenal. You only need to have a bigger brother than the ship you are protecting, and big brothers can have even bigger brothers for several tiers of flaming fun. Larger differences in size allows for some speed differences. Many races have more hardpoint positions on their smallest hulls, so this approach can be quite natural.
Be sure they're both in range at all times, though, or the enemy gunner's choices will be made for them. Bear in mind that different craft types can have different attack preferences, so the best big brother for a small frigate is another frigate, not a cruiser.
You know what's even easier to hit than a big moving spaceship? A stationary one. The Stoptank takes this to logical extreme by turning off it's engines to shoot while the rest of the fleet advances (or dances) around it. Best deployed in the periphery so they don't clog up your advance, Stoptanks can be used carefully to distract a few guns for a long time, or a whole hell of a lot of fire for a very short time, depending on your positioning and... benevolence.
Smaller ones will last slightly longer, Larger ones for absolute attention magnet. These can be surprisingly durable if you're only distracting a few guns each, so extra shielding and repair modules are a consideration. Note that heavily damaged ships can inadvertently become Stoptanks even if enemy gunners don't have vulture orders - damaged ships slow down to a crawl.
Go ahead and give some of these a shot. This article covers gunnery only - For tips on deployment and exploiting movement, try here.