The crew leveling system has been enabled in order to add a greater importance on ensuring the crew members that you take out with you make it back alive. Having a veteran crew greatly assists in the event of any events due to the ability to quickly generate needed systems and repairs.
Crew members gain experience while working on various systems on the ship that need improving. This occurs for things like raising the shields, repairing ship objects and even flying the ship to name a few.
As soon as a crew member gains enough experience to reach the next level simply open the crew management window, select the skills panel and distribute the point to where you feel it is best needed.
The morale system was created at the origin of the game to put a greater emphasis on an actual living crew. Crew members jobs have a direct correlation to their morale. You can force a crew member to never go on break but their health and morale will continuously drop. A crew member with the ability to produce 10 points of shields will only produce 5 points of shields when their morale drops to 50%.
Crew Perks... and Issues
Crew members have always had attributes that affect their gameplay. These attributes altered the amount of experience it takes to level, the speed at which they travel around the ship and even their ability to work as a team to name a few. The top issues and perks were tracked in order to show the difference in crew members at a quick glance.
This takes that system a step forward and based on the attributes of the crew members provide an additional perk such as quicker experience gain or someone who has low work ethic may ultimately have their fun meter reduced even greater while working shifts.