I think I already mentioned this - that's not how it works.
If you issue an intercept order on the enemy fighter, *one* of your nearby fighter wings (or fast frigates) will break off and go after it. If you need to beef if up, you could use a direct order to add another ship to the mix.
If the system worked that way, it'd be amazing. But it doesn't, unfortunately. The problem tends to arise when the AI makes really questionable decisions, forcing you to use your Command Points to correct AI oversights rather than to enhance your strategy.
Lets take the intercepting fighters example. I've given my capture orders and such, everything in the fleet is moving. But out of nowhere, a bomber wing appears on the left flank. I give the Intercept order...and it assigns a seemingly random Frigate from across the map to intercept them. I would much rather have my nearby Talon Wing or Point Defense Frigate do that, because they can certainly do it a hell of a lot better than my Brawler Gunship.
If you're gonna have the really general stuff, you need to tweak the AI, so that it realizes that Point Defense Frigates and Fighters are better interceptors than Assault Gunships. Or that my Close Support Frigate would be better at striking a Carrier than my Point Defense Frigate. IMO, the best way to do that would be to let the player add "Tags" to ships before a battle. "Tag" a wing of fighters as Interceptors so they prioritize enemy fighters and bombers. "Tag" a Frigate as Attack, Close Support, Assault, Point Defense, ect. So the AI would know what it's best at when auto-assigning.
And, for the love of god, stop making AI-controlled Fighter Wings ignore Bombers/Torpedo Bombers and charge at Capital Ships that they can't hurt.
The Command Point limit is the biggest issue. You can't correct bad AI decisions without wasting several Command Points. I cringe when I see my Talon Wing targeting a capital ship, my Carrier trying to intercept a pack of Frigates, or my Pirhana Bombers trying to Intercept a wing of Broadswords...
Other issues that need addressed:
1) Damaged ships don't seem to know when they need to get out of the fight. I frequently have to order Fighter Wings to manually Repair and Refit because they won't do it on their own when they're all almost dead. They tend to wait until only 1 ship remains before repairing, even if all 3 ships have almost no hull left. Crippled frigates have similar behavior. I've never seen them retreat on their own.
2) Specific orders regarding Fighters. "Fighter Screen" for capital ships instead of general Escort (Would make the assigned fighters prioritize enemy bombers and fighters attacking the ship they're screening over any other threats.), and "Intercept Strikecraft" or something similar would be good for telling available Fighters or Point Defense Ships to intercept instead of assigning a random ship.
3) Some sort of self-preservation setting for ships that are heavily damaged or crippled. Or at least some notification that they're taking heavy damage. Currently, you can manually retreat them, but I usually don't even notice they're in trouble until they're dead.
4) The Command Points seem really arbitrary. If someone wants to play the Command System a ton to strategically win battles, he should be able to do that without having to work around the Command Point System. It really feels like just tacked on difficulty. A nice fix for this would be making Assign Task not cost Command Points. You'd be able to bolster orders and specify what you want each ship to do. And counteract bad AI choices (No, Talon Wing, you shouldn't intercept that Onslaught). Hopefully officers and character skills should help that, but it definitely needs tweaked.
5) Once an order is completed (IE: A ship retreated, a fighter wing repaired, a target you specified is destroyed), getting the Command Point back after an order is successfully carried would be a nice way to ensure that you can keep assigning points. Perhaps add some sort of Character-Based skill that does that if you design your character in that way?