Gaining Skill Points
You can gain Skill Points for all your classes by clearing Cocoon and Tower quests. Cocoons can be found at various locations around the map and rewards 1 skill point. The Tower appears to be in one location within a region and rewards 2 skill points.
hi
Hello
It's pretty annoying but you don't get any points for a perfect clear so it's not that hard either. Not sure what the point of doing the side missions even is aside from bragging rights.