There are exactly enough skills points available in the game to unlock all the skills so unfortunately you have to find all of them.
Firstly you need to complete the story gaining all the sync points as you go.
Secondly you need to complete all eleven co-op missions ( not the heist missions) and you will gain sync points for completing each mission.
finally you need to find all the 40 hidden sync points in the 11 co-op games. They don't automatically show up on your map so once you are in the general area of one you need to use your eagle vision to pin point in. You can collect these sync points over multiple play throughs of the co-op missions and you can quit out of the mission as soon as you have found a sync point and it will register as collected.
You can track sync points collected through the progress menus.
Below is a video (not mine) that I found really useful for this trophy.
Also I have seen comments on forums that this trophy can be glitched and not unlock so as this game auto saves your progress I highly suggest backing up your save to a USB stick before unlocking your final few skills just in case.