I agree with some of your observations, and I have some suggestions and some of your points I have no comment on. Diving into the list:
0. To alleviate my not knowing how the controls work, and because I am not interested in reverting to old games, I have set autosave to save every season. Then, if I click and my unit goes running off in the wrong direction I can restart that season. This gets tedious but I consider it essential while learning the game.
1. Yes, this can be a huge issue. See my point 0, above. Also when you have your mouse over a piece of terrain you can see how much movement you will lose for moving into the tile (0.5x means you will lose 2 moves, while 4x means you will lose a quarter of a move and when your moves reach or cross 0 that units movement and ability to initiate combat ends for that season). For now, it is best to move only one tile at a time.
2. This also displays your tax rate and mouse over gives you some breakout. Also, if you go to the "Govern" screen and select "Ledger" you have the same widget, along with "City List" and "Economy" which give you further details. And, yes, running your economy is really that important (though you have multiple "right courses of action" with tradeoffs which depend on how you play the game. For now, I would just pick something that feels right...
3. Before I discovered that tooltip, I would hit "ok" instead of "use" and then go to the units "Equip" screen where I would mouse over the item to see its details.
4. Until the improvement is built, it's just a framework. But it does get added to the city. The details of what you see depend on how you have your options configured.
5. I wish that text would change to "Read Tutorial" when there was no video. I also wish that the help information contained details which are currently missing. If you have time it would be valuable, I think, if you wrote down a list of unanswered questions you had after reading or watching each tutorial. There is just so much about the game that I have had to learn from playing it, and now I suspect I would not recognize most of the gaps... But, also, I am too lazy to build that kind of list.
6. If those strategic bonuses are spells then they will need both mana and essence (a variable amount of mana, with a very few costing zero, and 1 essence per strategic spell). If they do not show up in your spell list they typically are for the city that the NPC is in (unless the description says otherwise).
8. I usually move closer to the border so I can see something inside it which will tell me the owner of the land. Note that this will make the opponent sovereign aware of me if he was not already aware of me (and if it's a sovereign that owns that territory).
10. You do not get the benefits from an improvement until after it is built. (However, you have to pay any up front costs when you put it into the queue to be built, so usually it is best to not have a deep queue.)
11. This might mean that your enemy has no idea where you are, either, depending on how good their scouting has been. Enemy rulers declare war for their own reasons (which you can get an idea of by going to the foreign relations screen -- motivation might include things like "I'm paranoid" or "today is a manic day" (though the latter seems to be a motivation for peace rather than for war) but also can include things like "your army is weak" or "we have a different allegience".
13. This typically means the city is already in view.
14. I think that there is a tooltip somewhere but I forget where. There's plenty of room for improvement here.
15. Yes. See also my point #0. Once you have an idea of the improvements you can also include your next planned improvement into the name of the place. Edit: apparently you can also move the map with the arrow keys? I need to try this...
18. Dark green is often something other than a sovereign. You can see the color code by going into "Govern" and selecting Foreign Relations (unless you have enabled "smart player colors" under advanced options).
I played through on easy my first time through, and that was challenging enough for me because I did not know what I was doing. I then set it to one option lower than that, and that was not any easier for the start, but none of the other sovereigns improved (so I quit that game because there did not seem to be any point in playing it).
Note also that you can research improvements, unless you are playing Altar (or a custom faction you have designed for this purpose) you are probably need to build a civilization to support your research efforts and your research choices will be important.