Endless Space has a roshambo combat system with beam, kinetic, and missile weapons and their corresponding defenses. What is the idea ratio of these defenses based on the typical AI opponents? I seem to see a great many beam weapons employed by the midgame with kinetics early on but rarely missiles and yet the Auto-Build likes to put Chaff on my ships for some reason. Is this just something I'll have to get a feel for?
The first ships the AI makes will always be ballistic, because it makes some defensive ships asap and that's the only technology available to it at the time.
From peaceful races you have more chance to see a lot of ballistic because they tend to research other areas that fit their play style better (production, growth, diplomacy, happiness, etc). But when you are facing warlike factions, you will see more variety of weapons because their "war technology budget" is higher. This seems to be especially true for Hissho and Cravers, then empire to some extent.
Another factor to this is the difficulty level. You will see more variety the harder mode you use. I play on Serious and i tend to see a lot of variation in weaponry. In my current game my Hissho enemy has mixed ballistic, missile, and plasma weapons all in the same fleets he use against me.
So yes, you have to get a feel for this and scout properly. You can suicide a scout ship from time to time to check, but if you play on higher difficulty it is generally better to build ships that are ready for all situations. The most common strategies you find are :
1) A swarm of destroyers with weapons only and no defense. The idea is to play a kamikaze tactic and keep producing them non stop. 2) Using battleships with very high resists so they become near invulnerable to damage. The ratio is about 2/3 of the weight in defense.
My preferred tactic which i developed is not very popular, perhaps simply because it is not known yet, is to make missile boats with no defense modules other than the extra health from support. I do 1:1 weapon to health modules, focus on +health techs, and use the repair card every time. The idea is that with more health, you get more regeneration from repair, thus can survive the first and second phase of battle, while your missiles will almost always kill the enemy on phase 1 with the massive burst damage.
I hope this has answered your question. Good luck with the game.
I recommend building several different classes of ship. You will not be able to build the most effective fleet with one ship class.
To begin, I'll assume it's late game and you have unlocked all your ship hull types and at least mid-range military tech, and that you have access to the core military resources (titanium-70, orichalcix, hyperium and adamantian).
I created four core ship classes for my fleet, all of them leviathan-class hull; you will need more ship classes if you don't have the largest ship class yet.
Command Cruiser (CC): give it 2 Armor modules, 1 Repair, 1 Power, a small number of long range missiles as space permits, and lots of shields and deflectors. No flak. This ship can contribute a small amount of firepower but is mainly there to repair the fleet and use its Power module to boost the fleet's weapons. If you need additional support, load up a fighter or two on it to shoot down enemy fighters and help a little during invasions. If you'll be traveling far, stick an engine module on it to give your fleet a speed boost.
Dreadnought (DN): give it 1 armor, a few of each defense but leaning toward flak and shields. I personally love long range kinetic weapons because they fire so many times per round, and hit so fast, that the enemy ships are dead before they have a chance to fire all their volleys. The main goal of this ship is to dish out kinetic damage. Pew Pew!
Carrier (CV): definitely give this ship the max number of fighters/bombers, in the proportion you deem necessary. If the enemy isn't running any fighters of their own and you already have invasion covered, use battle bombers. For the best general loadout, use 2 fighters and 2 bombers, both balanced. You can allocate the remaining space to weapons and defenses, but I recommend long range kinetics. 2 armor modules will almost guarantee that your carrier lives through the battle.
Troop Transport (TT): the siege invasion module and troops are the main features of the TT. Aside from that, make sure it's well defended with defense modules and armor. Doing damage is not very important because your DN and CV will lead the charge.
When ordering your fleet, ideally the order will be DN, CV, CC, TT. That way if the enemy decides to focus fire your first ship or first 3 ships (Nosebreaker), the TT will not take any fire. If the enemy spreads fire like usual, your ships should be defensible enough to survive the assault.
The crux of this build is the rapid repeated volleys of kinetic weapons streaming out of your DN and CV in the long range phase, allowing you to cut the enemy fleet in half if not outright kill it before the enemy can close range. If you have a dedicated battle fleet, you'll run 2xDN, 1xCV, 1xCC and 0xTT. If you also want to invade, you'll only have 1 DN, and a TT. This assumes 16 Command Point cap - if you have more, use more DNs or CVs. If you have less, the CV is not strictly required, but the CC and DN are most important.