Well, Reaper, it depends. Although I would love to have practical uses for each unit, there are some boundaries that just cannot be crossed. Even if the cavalry is upgraded a bit far than the pikemen, pikemen still destroy completely cavalry. You see, in the example I used, the only use for cavalry was for passing nearby and damage using trample, only getting one attack or something so that they wouldn't die. The most used units there were archers, then warriors, and just then the knights.
Also, I wish a opinion about the name.
And Goffterdom, could you write in a list all of your questions and etc right now? For example, in a page after the last time I posted you said you had doubts about resources. Now you already have the idea of Raw Materials... Well, just list whatever you need help balancing/brainstorming/etc with. And if you think it is solved, make a new post with it with the issue removed. Or just do it in the 1st post, so we don't have giant pages of list of issues that are slowly decreasing in size.
Edit: Moral System's box's name is written Click to Reat. Also, you said you needed a lot of help on your Resources tab on the 1st page. But it does not mention the Raw Materials, so I don't really know if that's outdated. Again, that list I mentioned up above with ALL the issues (could also be separate lists triggering/terrain ones for other types of colaborers... A example? You said yourself you don't know if somethings are Doable, so triggerers could help you in that.)
Also, let's see what else can I think of...
About raw materials, you should propably be able to do manufactured goods with them (buying them using wood). And maybe they could sell for gold somehow. And/or be used for something (needed for a tech?) so players may like to buy it as well. Everything you actually wrote about are pretty nice right now, so I can't think of anything to improve those (except resources, but then again, we have the issue I stated above.)
Age System: I can't think of anything that really could work about it except the basic. The basic is that it is an upgrade (So when your capital is destroyed you won't get all the way back to Dark Age again), it have pre-requirements, and are just really important. The LoE's ages's names are pretty ideal. (For instance, remember my farm idea? Also remember that it would have a important upgrade in the 2nd age? Feudal Age isn't pretty much farming and walling (historically)? Aside from the upgrade, it could have an upgrade to walls. Like, a big one, Feudal Age's specific.) What I though about is that when you upgrade to a new Age, you would gain some kind of benefit (so instead of researching it, you automatically gain a bonus to wall's armor and health when you upgrade to Feudal Age).
Ah yes, although I know that siege engines are supposed to be extremely difficult to handle, do you think there could be a realistic solution to make them move faster? If they are as... Difficult as you describe, they're going to slow the army so much that until reinforcements (siege accompanied) arrive for example, the 1st forces would already be dead. Also, decrease the collision of units to a minimum, so it is easier to maneuveur them in battle. Of course, they wouldn't have 0 collision, for it would be just too... Weird.
Influence System... Wooray. Ah, the days I suicided my own armies so my enemies would lose cities and be overwhelmed.
A balanced system will be hard, hard, HARD. Although it is not supposed to be subtle or too easy as well. Geez...
I can't really think of anything like that right now, except for the already proposed systems (the original system, Garrisons, etc.)
Moving on... Heroes. You already covered them a bit on Warfare, so... Let's see. After gaining some experience in battle (which is a bit hard, really) your unit becomes a High Ranked version of that unit. I think that of all buffs it would recieve, aside from Moral bonuses, would be to be more durable, since you worked HARD to make that unit actually survive two or three battles. It should propably have a aura that increases both mana regeneration and armor.
A Hero, however...
Heroes are way more... Berserk than High Ranked units. While the 2nd thrive for survivability, the 1st are there to make a difference. A big difference... In the number of enemy corpses. While they maintain the mana regen aura, they will win a command aura instead, (well, depends on the hero. Archer hero would win ranged damage aura instead?) And offensive abilities. But I have almost no idea about what would they be. A classic, Swordsman Hero could have (depending on the total number of spells) a basic damage aura and... Cleave? Ah, I really don't know. But I did though of a good skill for a could-be Paladin Hero or something. Could also be a Priest skill (the Priest's would be a Shout type, with a duration. Paladin's would be a aura.) Blessed by God: Each hit in the name of God allows you to live longer (as you should have guessed, vampiric aura.)
Ship System. I know what you DO mean...
They would have no attack, just skills. The basic skill, use Cannons, which will fire to both sides (or separate skills for each side). Siege ships would have a attack (I think that some nations actually used ships with implemented Trebuchets) But they would be innefective against Ships. Or not. They should have a minimum range, though. More skills... Stationary? Increases attack speed and decreases CD of the other skills... But they simple do not dodge anything anymore. Or in case if the cannon balls really aren't dodgeable at all, decreases armor or something. Also, Grappling: depending on a number of factors, you could control a enemy ship. For instance, one could buy crew for a ship, which would be represented by mana! The bigger the ship, the bigger is their maximum mana. Crew dies as you take damage, and even more if the other ships specialize on taking crews out, as stated soon. The more mana you have, the stronger and/or faster your skills are, as well as the rate of success of grappling, which would also depends on the number of enemy crew. Some ships could specialize in taking out crew, so that the ship sinks actually of having no crew at all (dies with 0 mana) or are almost empty so that they could be easily taken over. When you conquer a ship your mana is divided into two and a half goes to that ship. Mana regens naturally near ports, but items that restore mana could be bought to make them grow faster. There could also be items for normal troops to regenerate faster (Beer!). And in case you're thinking "Normal troops aren't supposed to regen mana near Ports", Ports have lots of taverns for your ol' tired soldiers to rest a bit. Of course, mana regen would have to increase mana percentually to balance that out.
Battles would require so much of a player that I fear for someone which fights on two fronts. So I though of a pretty nice skill to help outnumbered players! A "Run" skill. Every living thing has it, and its use is pretty much obvious. Although... If you're running away from something, you are very likely to be a LOT easier killed than fighting. So running also decreases your armor. A LOT.
Whew. That was exhausting. I hope I helped.