I love many of your ideas on how Civ could be improved upon and changed. I'd like to give my opinions on some of the things I disagree with, or think could be implemented better, as well add other features that you didn't mention. I would love any feedback you or the community gives me!
Game Philosophy
Standing the Test of Time
I really like your ideas on trying to survive for extended periods of time being a struggle within itself, rather than being expected. The problem with this that you addressed is that players will struggle to get to late game, discouraging less experienced players. You suggested the option to start later with bonus techs and units, which I like, and is partially implemented already. My Idea would be to have an option to start the game when the chosen civ started in history. For example, if you chose America, you would start under the control of Britain (or another Civ, depending on settings, possibly random), with the cities, units, techs, and the goal to secede. This would give the alternate view on the Revolution idea mentioned in Expansion (which I love and wished was implemented since I started playing civ V).
Unit and Combat System
Resource Limits
For the most part I liked your ideas to counteract the SOD and LOD problems. I also like the ideas to put units to “sleep” making them use less (not none though) resources. My only major disagreement with this section is the non-rival usage of resources i.e. iron allowing 10 swordsmen and 10 axmen. I think you should be able to distribute your resources amongst different type of dependent units how you want, especially with the benefits provided by balanced military stacks. This means that 10 swordsmen and no axmen will overall be less beneficial than 5 each.
Environment
Resource Depletion
I like the idea of over usage of farms leading to problems as long as it doesn’t happen too fast. I think strategic resources should be used in a different way though. Rather than an overall value that describes how many iron tiles you control, resources should bank with each resource only holding a certain amount. Units would take a larger amount to build and would require a small maintenance fee of gold and its resource to function well. This will take balancing to get good stockpile amounts, fees, and extraction rates, but I believe it would be more realistic than the current methods of non-renewable strategic resource allocation.
Expansion
Self Founding Cities
I like this idea but I think it needs more depth than what you described. I feel like the cities would have to have a specific reason to be founded. These could be religious freedom (like the Plymouth colony of Britain), lust for wealth (Jamestown), or just a new life (Oregon and the Oregon Trail). These cities should lobby the government or different corporations for funding and charters for their new colony. Government Charters could lead to extra profit from taxes and resources for the government. The colony might still be created without a charter, but might not be as friendly to the civ V. I do like the idea of forts eventually growing into cities themselves. Forts should also automatically “claim” the land around them discouraging other Civ’s from expanding to close.
Public Works
I really like the potential of this idea if you can decide as the player how much production tax is taken to produce improvements.
Science
Blind Research
I really like the idea of Blind Research. I think there should be another option though: reverse engineering; the ability to research a specific tech if you see a unit or building from it from another civ, or if your spies discover that a civ has it.
Traits and Abilities
Unique Leaders and Abilities
I like this idea, but it would be cool if each Civ had multiple possible leaders that you could choose from at the game start (i.e. Washington, Lincoln, etc.).
Adaptive Traits
I don’t think Civ6 should entirely remove the civ specific bonuses, that would remove too much of the historical background of the game. I like the idea of adaptive traits though and I think they both could be implemented. Rather than switching entirely on turn 70 though, it should be gradual. As you use certain aspects more, you will slowly gain benefits for them, losing old benefits (slower than you gain them though).
Religion
Religion is the only section where I disagree with you on more than a few points
Self Founding Religions
I think the religion should be loosely based on the religion for Civ V: G&K. The only problem I found with this for founding religion was the rush needed to guarantee the ability to found your own religion. I like your idea that Religions found on their own, but there should be some way to influence the odds of one founding in one of your cities.
Spreading Rates
I agree there should be some way to balance the spread of religions, but I propose a different method. Rather than extra missionaries, newer religions should get a flat bonus to its spreading rate. Nothing enormous, but it would help balance out the advantage of starting earlier, as well as give some reasoning to not push for religion as early in the game.
Schisms
I agree with the idea that schisms should occur, but your proposal is too drastic in my opinion. Rather than half the cities randomly converting, it should start as one or two cities where the religion is most unnaturally pressured (with inquisitions or military enforcement). These cities would be resistant to conversion for the next few turns,
Inquisitions
One thing that the inquisition idea needs is a civic that describes religious freedom. There shouldn’t be any likelihood of revolt for religious reasons if the Civ allows all religions.
Wonders and Super Wonders
Super Wonders
I love the idea that the previous victories aren’t game ending goals anymore; instead they are just big projects with large bonuses. This would allow for advancement into future eras and possible colonization of other planets.
Extras and Scoring
Unlockable Features
I like the idea of Unlockable features for added replayability, but they shouldn’t be powerful enough to be game changing. Imo, much of the unlockables should be aesthetic, and it shouldn’t be possible to pay for them.
Features Which Won’t Return
Tundra Farming- I agree, but it should be possible with tech upgrades
Espionage – espionage should be implemented, but I agree it wasn’t done well.
Additional Ideas/Thoughts
I have three major ideas that would drastically change the game. I plan on making another thread centered around these ideas eventually, but for now I’m just going to post them here (I’ll link to it later if I make one).
Time Lag
This is my biggest idea for change. This is based on the idea that before the internet, it took time for information to travel long distances. The idea is that the further away something takes place, the more time it takes for orders to reach units and cities. As techs are discovered that increase the speed for information travels (horsemen, roads, railroads, caravels, telegram, internet), you can see further beyond your capital and carry out orders quicker.
This would drastically change the way Civ functions. It would force players to plan multiple turns ahead for what a city should build, and delay the income of information (size of cities, techs researched, production finished etc.). It would help with the problem of ICS by limiting the expanse that a Civ could control early game. It would be similar to the idea of fugal Europe where kingdoms couldn’t be larger than one day by horseback in any direction without major communication problems. It would force players to send out units on a mission, not knowing if they succeeded until they return, if they return. Scouts would require extra defense from barbarians because the maps they make are useless until they return.
Communication can be increased through multiple methods. Messengers can be sent with orders for specific units or cities, or diplomatic information between Civ’s. Players could also choose to move their leader (a new unit) to a different city or location (with heavy protection, death of a leader can have drastic consequences) to better manage a growing city or command an army in the midst of war. Great generals can be used as a second “vantage point” allowing you to instantly make orders, giving great generals a much needed boost in functionality. As technology progresses, players can lay out telegram lines to allow instant, but limited (only influence a few tiles away from line), communication between cities or units. Radio would allow another boost, letting radio towers influence tiles near them. The discovery of satellites could allow for influence over the entire planet.
Because this would have huge effects on game play, there should probably be an option to disable this feature, but I believe it would benefit the game.
Outposts
My idea for outposts would be a unit (such as a merchant) would found a trading post (similarly to a settler). Players would build trading posts near resources to connect them to the empire. These posts could also have the ability to charge other Civs to pass through them (Panama Canal). The advantage to the trading post would be: cost, merchants cheaper than settlers; no unhappiness problems; and the potential to grow into a city over time.
Other Planets
This idea is fairly straightforward and I highly doubt I’m the first to think of it. The discovery of space travel should open up a new era of gameplay. You should be able to colonize other planets. I was hoping for this with Beyond Earth, but was sadly disappointed.
Thank You
Thank you for reading my suggestions. Feedback of any (hopefully positive) kind is welcome.
I’m especially interested in what people think of my “Time lag” thoughts. This is an idea that I think has great potential, and I would love to see it implemented.
Here is a link to the main thread
http://forums.civfanatics.com/showthread.php?p=13434860#post13434860
Maybe start a new thread "Time Lag Idea" or something?
It could have however created interesting situations, like : an outpost in a special unit that costs money as any other unit. You put this unit on any improvment and the resource is yours. When another civ plants a city nearby that includes this tile, your unit is moved out as any other unit would do. Now you have a special window that appears when this happens : you have two choices : let it be, or declare war with a disminished reputation impact. Maybe every unit could be an outpost, triggering early interesting choices like having a better functional army / scouts or more resources. The only problem is when a barb archer comes in range and fires at the outpost. Maybe resources could transform your melee units to range units ? (or switch their ability, melee units now having a range caracteristic) Could be interesting for conquest wars.
, I plan on making a thread, I just needed to get my idea down somewhere
Seems like it would have to include a detailed "instruction-giving" interface for the scouts/soldiers if they are to go off and do stuff for a few turns without human control. Maybe that could even hook down to scripting with LUA or something. I've always wondered if actual coding could be brought in to a mainstream game as a core gameplay element (strongly doubt it though 
