I'll take on a few things at once here:
Flanking is obvious, give advantage to the troops that flanks the others.
agreed, for open battle. (I.e. its pretty easy to flank a squad in a base, but you shouldn't gain an advantage for it.)
Good idea, in general, this is a good tactic.
Ambush is great way to use terrain and other features, if the enemie ambushs you, you could make the defender troop panick spread and lose morale.
being closer to a blocking item, like a vehicle wreckage, or a tree line that is in between the shooters.
Squad positioning also could take relevant input, if you go straight on with your melee warriors vs a group of ranged, while on range the melee would have advantage, maybe breaking the ranged units formation, no one would stand there to die In a field where you have a bow and knight is right next to you. So you could make units behave more human like, fleeing and etc.
agreed. So in a tree line, bowmen might would have a significant disadvantage over swords men in close combat. But bowmen with good climbing skills might gain an advantage, given a moment of time's head start.
This gives chance to another aspect, make the player be able to set up unit tactics. Like attack while the melee are not on range, once they get near, fallback and move the infantary forward.
Simple commands like that could create a great combat experience. You could have each squad be lead by a General, an depending on the experience of the general be able to setup a larger queue of tactics.
I like this as well. I've been considering the idea of officers, who will run things in your absence and without them, your troops mostly just go after basic goals with no cohesion. But officers can receive training, which is basically just upgrading their AI.
Another idea that could be implemented is in the range wepon department, make the units go out of ammo, and need to reload (a few time without attacking, or going to get ammo), this would make players that know how to play to make the enemy use their ammo first, and attack while a opening is done. Or maybe the attacker could wait till the right time to call their ranged reinforcements and caught a player out of position.
Excellent. Several people in other posts have also brought up the ammo reloading issues. And Supply lines. I want to make sure that requiring reload doesn't remove from the fun, but I think it can be done.
Missing, the veterancy of units should give an idea of how effective a shot they are or how useful they are with their weapons in general. If the progression of unit veterancy is done right then the player's mouse speed and hotkey use should increase inversely to the time it takes for a battle to happen tactically. Cover and missed shots fired are the key to this. Better player, less missed shots fired.
In addition to having increased damage, perhaps also that they now to take immediate cover when a surprise attack starts. And perhaps healing is done by just having some medic in a space suit spray you with stuff.
The only way to reduce the effects of apm is to make micro irrelevant. If the player only has the power to set up hierarchies and send units to locations with generic orders and maybe some settings they only have a limited amount of clicking to do.
This is a concept I've been struggling with. I mean I understand it, and using AI and Officers to take on tasks, however, I feel like it can be done. Oh, here's an idea towards that: In starcraft 1, if you just sent troops to a position, they would walk through anything without taking heed to damage they took. but if you told them to attack a target, they would also stop along the way to attack other things. Perhaps other hotkey attacks could include certain strategies to employ, like sneak up, take cover, attack from cover, provide a distraction first, then attack from the other side. Different command strategies where you still tell them what to do, but they will take some AI liberties. But you as the player define what, as they do it.
You should not put tactics and strategy words in the same sentence, these are very different things.
I am aware they are different, which is why I have 'and', similarly to how you used both words in your sentence, and tied them together with the word 'and'. 
Or to put it shorter, you can't at the same time simulate a whole nation's army (10 million soldiers) and order which one of these individual soldiers shoots at whom
I do agree with you here though, and understand the key points you were making. Managing macro and micro is hard to make work. But lets say it could, what would it take? I'm thinking of Clone Wars, where you keep coming back as another robot or clone, into the same battle field. What if every time you died, before coming back in, you could influence where troops were focused? You would employ a 'strategy' that most other AI's would follow, and then actively engage in the same strategy yourself. However, this is not really what I have in mind.
I plan on letting things be handled by AI, but that a player can zoom into any level. if they are focusing on a smaller (yet important or fun) battle, other AI's will handle larger scale strategy and vice versa. The player can get away without knowing all the keyboard shortcuts to employ strategy, but if they learn them, they can get their troops to do better than the AI, perhaps.
Another feature you can implement would be terrain bonuses to attacking and defending, possibly differing for different races/units. Also give bonuses for morale from squad commanders - it's a random chance that the commander dies, and then perhaps there'll be a chance for a regular squad member to step up and take command, but it'll be unlikely the unit can be saved.
I definitely agree with the use of the terrain, and a few other posts have mentioned this as well. What I like though is someone lower in rank stepping up to become the officer. perhaps you could spend money give additional troops officer training, and that they can change roles to an officer if needed. An interesting feature. It would cost more for the extra training, but if needed, could be invaluable for uninterrupted strategy.
