Ah, ok. That makes sense. So now capturing objectives is only good for giving you command points? And how possible is it to get your max CR to 100% because mine is never more that 65 usually?
Objectives are for CP, or damage boost, or speed boost.
In 0.6.1 the speed boost will be lowered but will apply to all classes and will make you ignore nebula's effects on speed.
For ships not controlled by the player the max is 80%, with an elite crew.
If the player ship has an elite crew and you have the Combat Aptitude at 10 the max is 100%. 2% per aptitude level, as well as a decrease to the CR per deployement.
CR controls all the stuff that used to be controlled directly by crew earlier - manoeuvrability (speed, acceleration and turning bonus), damage taken, rate of fire and autofire accuracy. If the ship is above 50% CR it'll get a bonus there, otherwise a penalty. If you're below 50% CR there is a proportionate chance of engine/weapon malfunctions, and missiles will not be fully loaded with ammo.
I'll let you work out the implications on the performance of a ship with a large per-deployement CR hit, right after a battle in which is has taken hull damage (this also decreases CR).