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Paper Beats Rock, Intergalactic Style
In comparison to a true real-time strategy game, the combat aspect of Galactic Civilizations II is not complex. This is a 4x game, and this means that long-term strategic planning, not short-term tactical combat, is the focus of the game. That said, it is important to make sure that you have as much of an edge as possible whenever you go into combat. Even if you're more about economic power than military might, think of it this way - every ship that is lost that could have been saved by better planning is wasted resources. Up in a puff of intergalactic smoke goes five turns worth of industry that didn't need to be lost.
At their core, weapons and defenses in Galactic Civilizations are extremely simple to understand. Each weapon type has a defense counter, and there are three weapon types and three defense types. This would seem to give weapons an edge, since you'd be less likely to randomly pick an effective defense against an unknown opponent than an effective offense. Defenses are still effective against weapons besides the type they're designed to defuse, but their effectiveness is only reduced. In truth though, both defense and offensive have advantages in certain situations.
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On The Offense
Most new players to Galactic Civilizations II pick heavily offensive ships over heavily defensive ships. This is for two reasons. One is that weapons seem more effective in the early game. It is difficult to spend on both offensive and defensive technologies within the first fifty turns, and you have to have offenses if you're going to do anything in combat. Secondly, the computer tends to rely far more on offensive ships than defensive ships, and players - getting their butts kicked by the game's relatively good AI - mimic this.
It isn't a bad habit to mimic; offenses are very powerful. The fact that each offense is only countered by one defense means that you're rolling good odds once you dedicate yourself to a weapon type. In addition, the early game really is all about offense. It just isn't practical to invest heavily in both offense and defense technologies until the roots of your empire are settled. Heavily offensive ships are more cost effective, and even if you do run across someone using the right defense, they rarely have more than one unit of defense. If you have two units of offense, you'll overwhelm them easily.
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Countered by Shields, beam weapons are the easiest to fit on a vessel. Their base size is the smallest among all weapons, and miniaturization furthers this advantage. The main benefit to this is flexibility. There is a hard limit on the amount of space you can have on a vessel, so the smaller each weapon is, the better. For example, let's say you have a choice between a Laser which takes up 5 space and does 1 damage or a Missile which takes 10 space and does two damage. If you only have 26 units of space on your vessel, you can cram more firepower into it with beam weapons. The flip side of this is that beam weapons are the most expensive of all the weapon types. You can certainly cram ships full of them, but you'll be paying slightly more for the privilege.
Countered by Armor, projectile weapons are the happy middle ground. Projectile weapons are not overly expensive, nor are they exceptionally small. If you're simply looking for a good, general weapon type, without wanting to go to far towards either miniaturization or towards cost savings, then the projectile weapon is the weapon for you. Personally, I find their indecisiveness a bit boring, but don't let that stop you.
Countered by ECM, missile weapons are the largest and most cost effective of the weapon types. They scale up in damage more quickly than any other weapon type, but they need to, because they are nearly twice the size as most beam weapons. This can make them difficult to fit onto ships at times, resulting in designs that don't have as much power as they would be able to carry if you'd been using the other weapon types.
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Defenses are only considered to be a counter against one weapon type. Defenses work at "full" effectiveness against the weapon they are meant to counter. They still operate at 1/3 effectiveness however, against weapons they are not meant to counter. As a result, defenses can be effective even against weapon types they're not meant to counter. You simply need to lay them on thicker.
As a result of this, defenses tend to become more powerful as you move throughout the game. Defenses are expensive, but they're also small, and as ships become larger it becomes easier and easier to build ships with absolutely insane defense ratings. Defenses also are more effective on larger ships because those ships have more hitpoints. This means that whatever damage does get through your defenses will have to do more damage to actually destroy the ship. As a result, defenses on a ship with very high HP make more sense then defenses on a ship with low HP.
Unlike with weapons, I am not going to go into the details of defenses. They are all nearly identical, with the exception of what they counter. Shields counter Beam Weapons, Armor counters Projectile Weapons, and Electronic Countermeasures counter Missiles.
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Putting Things Together
So, now that you know the basics of what defenses and offenses do, you probably want a straight answer; which is better?
It depends on the stage of the game. Offense tends to master the early game, for reasons that have already been outlined. Small ships are just better off with offensive weapons. You need some offense in order to take down an enemy after all, and at the early and mid game it is very important to take down enemies as quickly as possible, so that they don't take down your ship's hitpoints in prolonged combat.
As the game progresses, defenses begin to break even. They start to become superior at the point that you have access to Large size hulls. The small size of defenses, combined with the gobs of space available on Large size hulls, creates the possibility of making a nearly invincible galactic fortress, capable of repelling all attackers. I have frequently used high-defense dreadnoughts to tank numerous enemy battleships. These fights will be long, because the flip side of making a high-defense dreadnought is that your offense will be no more dangerous than a kitten's. However, if your enemy's offense has no chance to penetrate your defense, then it does not matter how long the fight lasts, nor how many ships attack you. Your victory is assured.
So there you have it. Offense early, defense late. Not everyone agrees to this assessment, but you could do far worse than follow this rule. At the least, you can rest assured that the AI will not be able to counter your high-defense late-game dreadnoughts, making the galaxy yours to conquer as you see fit.