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.