Mostly I agree with you in this thread, and appreciate you digging up (nevermind where from) the discussions in the OP since they're more outside the box than you usually see on this forum.
However, I disagree on the CP point. The concept of CP is not trash; the implementation is sub-optimal.
One of the dumbest things about RTS games is that you can micromanage everything as the king/admiral, and give orders to a distant spaceship, soldier, zerg, or whatever like every second, as though you were dragging them around on an invisible leash, without any regard to communication difficulties, attentiveness, etc.
There is no way a spaceship crew can function if their admiral is changing and belaying his own orders every second ("go here... no, go here... no, go here"). Carrying out an order/objective on a big ship involves a long chain of command and tens/hundreds of people from the admiral to the captain to the mates to the NCOs down to the guys carrying ammo back and forth etc. It just isn't possible to rapidly and continually change orders that much and not confuse everyone in the ship.
Also, it's really boring and stupid from a gameplay perspective. When you give an order in real life, you say "go and do this" and you leave it to the subordinate as to the specifics because they are trained for what they do. In RTS games though, you've got to micromanage for best results, basically stepping into the unit/ships body to get it done, by clicking a million times. You're basically just flipping between shoddy 1st person control of a bunch of units, rather than actual commander level decisions.
So I like that the developer tries to address this issue with CP. However using it as a pooled resource is a little problematic. It would make more sense if each individual ship had a sort of timer on how fast you could give it new orders, with little ones being more responsive and big ones being less. Your own flagship's capacity to distribute orders throughout the fleet (number of communications officers, etc) could also still effect things as well.
The CP doesn't address any of the issue you brought forth.
Different/conflicting commands? Not a issue. I happens in real life and orders change as the situation changes.
The only real effect of RL orders is latency and time. I takes time to give order and time for them to get executed. Neither can you give 20 orders at the same time (which you can do in a game if you pause). However, this is easily solved by implementing two very simple systems:
1) latency
2) order que
Basically it takes a few seconds (depending on factors) for the ship to start executing the order you are giving. This simulates the chain of command, communication latency, etc..
And order are executed in orders they are given. So even if you pause time and order Carrier A to attack, frigates B and C to fall back, once you unpause they won't immediately jump to.
first the carrier will recieve it's orders (that itself you should take 1-2 seconds at least) after which it will start executing it after 2-3 seconds
Once hte carrier gets it's order, the frigates will recieve theirs.
So timline
0 seconds - start, orders given in command interface, game unpaused
2 seconds - carrier gets orders
4 seconds - frigate A gets orders, carrier begins executing
6 seconds - frigate B gets orders, frigate A begins executing
8 seconds - frigate B begins execuing
If you ordered frigate A and B together as a group in the interface, then they will count as one (so both will act on 6 seconds)
Basically this simulates you verbally giving orders, like you are a captain, sitting in your chair and going:
"Comms, instruct the carrier Vengance to push the attack on the enemy destroyer! Tell frigate group 1 to pull back!"
Then your comms officer will relay those orders and then the ship captains would implement them