Welcome to the Thread,
@Duke William of Normandy! Interesting ideas well deserving of consideration here.
Having been involved in playing miniatures wargames and writing several sets of commercial miniatures wargames rules, may I comment that the 'soft' factors of Morale, Discipline, and Doctrine have been heavily addressed in these for several decades. They are also prime subjects for discussion in 'official' military and military history works going back even further, as in the US Army's 'Maneuver Control' manual for military maneuver umpires published back in Pre-Computer Era of the 1960s, which is full of statistics on when and how badly units might fail to carry out orders and why, all based on tactical studies from WWII and Korea.
To summarize, the 'soft' factors in military unit effectiveness are:
Doctrine: How the unit is expected to fight. This is very, very difficult to change, because it requires everybody from rank private to general to change how they use their weapons and formations and learn New Ways of doing things. On the other hand, it is Fundamental, because an aggressive or passive Doctrine can determine how likely a unit or army is to attack or defend, and Doctrine that does not match your and your enemy's weapons (as in, an Offensive infantry doctrine using massed bayonet charges in the face of massed machineguns) can lose the battle and the war faster than anything. A lot of Doctrine will be built into the weapons and unit types: a Swordsman simply does not fight the same way a mounted archer does, given the extreme differences in their weaponry
Training/Discipline: How Well the men can be expected to fight according to their Doctrine. Training and Discipline should be related factors, because the first task of any military unit training is to instill Discipline so that the unit will without question act according to its weapons training and doctrine. A poorly trained unit, on the other hand, is by definition Undisciplined.
An Undisciplined unit may not necessarily be Ineffective. Notoriously, the difference between Barbarian or Tribal forces and 'civilized' militaries is that tribesmen and barbarians have no unit training or discipline, but if their 'native doctrine' is a massed charge from ambush and you wander into the ambush, they can be devastating - see Teutoburger Wald and the loss of 3 Roman Legions to German tribesmen whom the Romans regularly mopped the floor with in open field battles. Training takes time, and more importantly, takes Gold/Money. Men cannot usually train as military units while they are also trying to earn a living, so the State in some way has to maintain them. And if the weapons require regular training, like complex modern vehicles and heavy weapons or swords, the State or some aspect of it has to pay the men All The Time. The difference between 'militia' or warriors that can be called up only for the fight and Professional Troops who train and are ready to fight all the time is a fundamental distinction in historical military units and armies.
Morale: How much the men feel like fighting. This is the most volatile of all the factors. Morale can change in a moment from bad to good or from good to "Run For Your Lives, They Got Elephants!" Well Trained troops as a rule will also have good Morale, but there are a host of ephemeral factors that can change that: have they been fed recently, do they have a history of victory against their current enemy, do they trust their General/Warlord not to Screw Up and get them killed?
Because Morale can change within a tiny fraction of a Game Turn in a game the scope of Civ (or any other 4X Grand Strategy Historical Game) Morale is very hard to directly model. For the most part, it will have to be assumed that, All Other Things being Equal, Morale will be a product of other factors: is there a Great General present? Is there a Great General present on the other side when you don't have one? Are you in supply? Have you beaten this enemy recently (within X turns)? Are you defending your last City or Holy City or Capital? (To quote William of Orange: "There is one certain means by which I can be sure never to see my country's ruin: I will die in the last ditch defending it", or even shorter: "Za nami Moskva!" - "Moscow is behind us!" for the defenders of that city in both 1812 and 1941). And, especially in a Holy or Ideological War, are you fighting a Traditional Enemy or attacking their last city, Holy city, or capital to Finish Them Off?
All of which means, in the 4X-type games we are discussing, there are some factors relating to Morale/Doctrine/Training/Discipine that should be in the game but are not in any of them now:
1. Professional versus Militia. Are the units capable of being 'called up' only for a war or battle but otherwise left as individuals in the economy paying taxes of some kind, or do they have to be kept formed and paid all the time? This will dramatically change both the Training/Discipline of the units but also their Maintenance Cost and their effect on your 'civilian' economy. It also varies with the type of economy: a pastoral culture in which virtually every man is a skilled horseman and mounted archer or spearman can call up a huge proportion of its population as very effective 'militia' compared to a city in which almost no one has weapons skills of any kind in their 'normal' civilian occupation.
2. Full Effects of Great Generals. IF you are going to have specific General units of some kind, which is a Good Idea IMHO, then not only their specific combat/movement effects on their own units have to be taken into account, as now in Civ VI, but also their effects on keeping those units supplied and effective and the effect they have on an enemy force without a General that has to face them, and the possibility that they can get themselves killed on campaign, an event which can very quickly kill the entire campaign or very materially change the possibility of victory (see death of Gustavus Adolphus in battle during the Thirty Year's War)
3. Doctrinal Changes. Right now, all Doctrine is Assumed, based on the weapons/unit type. This is largely correct - you can be pretty sure no swordsman is going to try to use his sword like a spear nor will a horse archer get a sudden urge to charge the enemy and beat him over the head with his bow. BUT these assumptions are less viable as the weapons get more complex. There were several different doctrines being tried throughout the 18th century as European armies grappled with how to make the best use of flintlock muskets in battle, and there are hundreds of books and articles in print on the differences in doctrine for tanks and mechanized forces in the 20th century, both tactical (unit) and Operational (Corps and Armies). A lot of these could be addressed with Military Policy Cards, which have the 'advantage' of being relatively hard to change, as Doctrine is.
I have read through your post, and I would like to add some things. For the morale thing, go check out Sirsquier in my thread, a Rework of the Military, He came up with a good morale system. For the supply issue, the War Weariness on Cities should also affect the Cities' yields. Since we are at war, we need to divert more resources towards the military and training rather than the domestic issues. About the doctrines, we could take a few ideas from HOI4. Hope this will be the start of a great adventure. 
