I understand what you're saying. War should not be made so costly that no one is willing to fight. What I'm hoping is that some kind of middle ground can be reached, where fighting consumes a large share of a civ's economy as in real life, but not so much that it is almost never worth it. After all, in real life, with real life costs, countries used to go to war all the time before nuclear weapons. I absolutely agree that if it is overdone, the game would be boring.
About the high quality weapons, the 3 type for each unit idea was just if the other would be difficult or impossible to code. Actually, I had a few other variants of this idea. First, the high-quality unit does not get any extra promotions on finishing production other than what it would get through barracks, armory, etc. Rather, all promotions are made correspondingly greater, so for example the shock promotions would each grant +20 or 25 strength in open terrain rather than 15. Alternatively, or additionally, the high quality unit would be given a special promotion that allows it to earn xp faster. This second would be particularly important if combined with the making units easier to kill idea. I also like you're proposal of a special project, its just that there needs to be some way of making the units themselves costlier to produce, otherwise they would be OP.