For missiles my general rule of thumb is 1/2 engines, enough agility to hit the speed your general targets are going at and a warhead strength sized on the square of the whole numbers. This would be warheads of strength 4, 9, 16, 25, 36, ect. The reason for this is that this is the point where you will penetrate another level of armor. Enough fuel to go at least 50mkm, and for your tech level probably more like 150-200mkm. Any remaining missile size points (msp)I will usually put in to either sensors (thermal) or defenses. If they don't seem to have enough eccm or it of a lower tech than yours on their ships for all of their fire control then missile ecm can make a big difference. For a bombardment missile I would use a drone and multiple submunitions with about a 50mkm range. The purpose here is to have a really long range bus and then lots of small missiles that saturate their point defense and get through that way. Missile armor only really works for really big missiles as you don't get any benifit from high tech with it.
For a point defense missile my standard is a 1 msp missile. .5 msp is engine, .01msp is fuel and a warhead strength of 1. the rest is agility. If your tech is high enough this will give you a agility over 100. In which case split the excess points to warhead/engine/fuel. A tiny bit of extra fuel will make for a big range difference, but the faster speed helps as well. The extra warhead just is nice when shooting at small ships/gunboats/fighters. I will often also make a design of missile with less agility, more range and a bigger warhead that can hit fighters or be used to shoot at ships if there are no incomming missiles to swat.
