I understand that there are many strategies one could implement in case of a failed assault or an unseen attack, but the truth is most people don't prepare to fail. -snip-
There are many quotes that fit this, but lets go with this one:
“Expect the best, plan for the worst, and prepare to be surprised.”
- Denis Waitley
A good tactician always has either an ace up his sleeve, or an escape route. You make a mistake and the game punishes you. That's how it's supposed to be.
The limit on command points is intended, and it is set low to prevent micromanagement.
Most engagements feature 4 structures, 2 on each side. You set the one closest to you on "Capture", the second one on "Assault" and use the last point to give your carrier an escort. By the time the enemy reaches you, you have at least 2 command points back (from the 2 structures) and can give more orders if needed. And if you stick to your fleet you can even see what's happening.