Generally, bravo! You have some pretty great ideas going here.
Here is a little more detail about all the ideas above.
Military Units - Balancing (done - just needs balancing)
As I see it there are 2 main problems with troops at the moment. The infamous spearman beats tank, and the I-will-rush-you-with-my-UU-and-beat-the-crap-out-of-you. Both of these problems have solutions. First of all, the strength of all units will change, later units recieving large increases. For example, a warrior will still have strength 2, a longbowman strength 9, a cavalry strength 24 and a marine strength 45. Of course, the problem with this is that you get jump points, where researching a new technology will double the firepower of your units. To prevent this there will be techs that will provide mini upgrades to your troops. As soon as that tech is researched all of your units of a certain type gain a free promotion which increases their strength. For example, an archer has strength 3, you then research mathematics which gives +1 strength archers, and now all of your archers and any future archers you build will all have strength 4. Also, with morale there is now another element which can be used to balance units. Preatorian could be changed to have strength 6, +25% city attack, +25% plains/grassland, morale 95, compared to swordsman with strength 6, +10% city attack, morale 85.
The "spearman-beats-tank" problem is more or less fixed in the current Civ 4 rule set. It really takes a LOT of spearmen to get a tank into a damaged enough state that it could lose, and even in the rare event that this happens, it will almost never turn the tide of a war.
I think you'd be better off introducing new units than "mini-upgrades." The problem with mini-upgrades is that they're both universal and free. This means that you can instantly upgrade your
entire army for the cost of
zero gold! That's overpowered. However, if you simply introduce more "in-between" units, then you can have a smoother upgrade path without changing the basic mechanics of unit upgrades.
Another possibility is to have promotions that get unlocked with certain techs.
I also think that when a unit upgrades, it should have all of its promotions refunded. This would have two effects: #1, it allows you to get rid of unwanted promotions from bygone eras (such as cover or shock); #2, it prevents units from obtaining otherwise "illegal" promotions (like City Raider Infantry).
Military Units - Morale (done - just needs balancing)
Morale is an entirely new consept to Civ. Every unit now has a morale, which is how likely it is to stay in combat and not run from the foe. Every time a unit runs from a round of combat, there is a probability that it will run from the battlefield. Roughly speaking, the probability is (100 - Morale) * OurHitPoints / TheirHitPoints. If a unit runs it looses 1 exp, and half of the health it had just before running. It will also move 1 square directly away from its opponent.
However, there is also a second darker side to morale. If a unit runs from combat, every unit in the stack it was in also has a chance of fleeing, and if one of those units flee, then every unit in that stack has a second chance of fleeing and so on, meaning it can soon snowball. When a unit flees not directly from combat it moves 1 square in a random direction and end its turn. Having a big stack can spell disaster, as your troops will scatter and can be picked off by enemy cavalry.
Interesting concept. The first (and biggest) consideration is whether or not you want to introduce a mechanic that takes unit control away from the player. Many players will find this feature VERY frustrating.
Also, because of the snowball effect, one failed morale check can spell disaster for an entire stack. This will lead to some wildly unpredictable (and lopsided) battles, and introduce a large element of luck into all battles between large forces. It's possible (and fairly likely) for a 5-unit stack to completely rout a 15-unit stack with a little bit of luck. If you think that the "spearman beating a tank" issue is frustrating, you ain't seen nothin' yet...
I think that Morale
can have a place in civ. The simplest solution is to give a die-roll modifier based on morale. In this scenario, both Morale and Hit Points are important in determining the outcome of a battle. Another thing is that Morale can be integrated with the "supply" system. Units gradually lose morale if they spend long periods of time in enemy territory without winning battles, and when "resupplied," the unit regains lost morale.
I really don't think that the Stack of Doom needs to be eliminated. Large stacks
should have a place in Civ. However, I
do believe that a large stack should not be the single "best" way to win a battle, and that there should be some advantages that you can gain by spreading out over large areas. Collateral damage is a partial solution to this problem, but it doesn't solve it completely. Increasing the yield of pillaging would also help.
Resources (not started)
This is quite a simple idea really, which should encourage players to controll ALL the resources, and not just the one's which they need for their army. For every different food resource a city has, it gains +1 food, but it can not gain more food this way than it has population. So, a city of 5 pop with access to rice, wheat, fish, crab, clam and bananas will gain +5 food every turn. The same will be true for strategic resources and production. Luxury resources will give +5% commerce each. To balance this out, cities will need more food to grow to the next pop level, and later units and buildings will cost more.
An interesting concept, but I don't see it as an improvement over the current system. Yes, resources would be much more valuable, even in the early game. It also means that civs that are lacking in resources will be completely left out in the cold with no chance to catch up.
It's far better to have resources affect the
limit of growth rather than the
rate of growth. Otherwise, the snowball effect of a civilization's growth rate will place too much emphasis on the early-early game expansion micromanagement, with no way to recover once you fall behind.
I do agree that resources should have more uses, however. Probably the Corporations feature from
Beyond the Sword will address this. Also, don't forget that resources already provide tile bonuses to any city that works them, so resources are already valuable from a purely "production" point of view.
Economy (not started)
I am not entirely sure how this could be done. A few ideas I have are to pool all of the GPP per civ, so every city will help you towards the next great person. Another one is to create a new world wonder called "East Indian Company", available with economics, with gives +1 commerce to each specialist. Any other ideas are welcomed, specialy if you can think of a 3rd way to manage an economy.
I agree that "cottage spam" is a bit overpowered. I think that having each cottage add .25 - .5

is a good solution, and better than having cottages directly consume food. With the

mechanic, cities will have a "grace period" when they can build a few cottages before hitting the

cap. It will also make

more important in more games, and tone down the Financial trait somewhat.
Having a centralized Great Person pool would be a good idea overall. I think. One thing you lose is the ability to guarantee
which GP you get, and
where each GP will be born, but that's a small sacrifice for the benefit of knowing that you aren't completely wasting GPPs by running one or two specialists in some cities.
Civil War (not started)
As well as generating normal culture, all cities will also generate rebel culture. The amount of rebel culture produced is a percentage of normal culture, and the exact percentage varies with population, unhappiness, unhealthiness, distance to capitol, number of cities, number of religions and civics. This rebel culture is kept hidden from the player, and does not show up on the screen until a revolution happens. A revolution can have many triggers, starting a war, changing civics, changing state religions and loosing your capitol in war. If at that time any cities have more rebel culture than normal culture, then the city will flip to rebel and so will some of its garrisson. If any cities flip then the rebel culture will become visible and cause unrest in the cities. When a city flips, it goes to a new civ called "rebel+nameofoldciv", and the rebel civ is imeadiatly at war with the parent civ. The interesting part of this idea is that it models both short term and long term causes, and large empires are more fragile and reluctant to change for fear of breaking up.
A very interesting possibility. If you decide to implement this, please DON'T keep the rebel culture hidden from the player! That would only add unnecessary frustration. Also, cities should have a % chance for culture flip each turn instead of a threshold after which a flip become automatic. This would bring the rebellion mechanic more in line with the already existing culture-flipping mechanics. You can also have rebels add

to a city ("We yearn for independence!"), the same way that foreign nationals yearn for their motherland.
The big question then becomes: what are the contributing factors to "rebel culture"? For example, if you make unhappiness add to rebel culture, then you end up with a snowball effect where your unhappy citizens create more unhappy citizens, and you lose your cities without really being able to do anything about it. This would also add more value to the Slavery civic (which is already overpowered), since the ability to whip away unhappy citizens would be
mandatory if you want to keep your empire from falling apart!
Another good addition would be the "Barbarian Civ" mod that Jdog5000 created. This mod allows barbarians to settle down and become full-fledged civilizations!
Reserves (not started)
Units in cities can be put in reserve mode. While in reserve a unit costs 0 maintenance but can not fight. It takes 2 whole turns to wake up a unit so that it can fight again. The number of units that can stand down per city depends on civics, technologies and buildings in that city. This should hopefully allow peacefull players to have a large army, but not pay for it while they are not attacking anyone, while aggressive civs will have to pay the full burden.
Interesting. This should not eliminate maintenance costs, but only reduce them. I think 1 turn is plenty long enough to "wake up," since you've already given up your fortification bonuses. Question: would reserve troops still count towards +

under Hereditary Rule? I suppose they should.
Supplies (not started)
There have been many models for supply's but most of them were far to complicated to be included in a civ game. This on is a lot simpler. All units have a certain amount of supplies with them. Every turn they use up 1 point of supply, and every time they use up 1 movement point or attack or are attacked they also use 1 supply point. Once a unit has no supply points in can not move or attack, but can only defend until it gets more supply points. There are 2 ways or replenishing your supplies. 1) spend a turn in a friendly city or 2) build a supply unit and use it to refill your supply points. Supply units use both hammers and food while they are being build and also require different resources depending on the age you are in. Supply units disappear once you use them.
This should make attacking other lands a lot harder and require the full effort of your entire civ. No more sending troops and then forgeting about them.
Unit supply is a very tricky concept for a game like Civ. Civ in general is not a tactical wargame, and really shouldn't be made into one. The scale of each game turn (which lasts up to 20 years at normal speed) suggests that combat is more of an abstraction than a simulation. The primary factor that determines victory should be:
do I have a stronger war economy? If the answer is "yes," then I should be able to win most of the time by virtue of bigger numbers and better technology, rather than better micromanagement and rules exploitation in the field.
That being said, it could be interesting to add
some logistical challenges to warfare, as long as it doesn't add too much unnecessary complexity.
If you're adding Morale as a unit stat, then attaching Morale to the supply mechanic would be a convenient solution. Units can lose morale (and their ability to win battles) the longer they remain "out of supply." This can also apply to cities under siege, where, if a city is cut off from the capital, it is considered "out of supply," and suffers the same morale loss as out-of-supply attackers.
Pillaging should also resupply units.
As far as the "supply unit" goes, I nominate Workers. Maybe one of their improvements can be a "supply camp," which acts as a supply source for soldiers away from home.
One more thing I would love to see is a mod that balances the civics a bit more. I'd like to see Serfdom as a viable alternative to Slavery, and to see Free Market and Environmentalism as viable alternatives to State Property. Bureaucracy is also somewhat overpowered compared to Vassalage.