It took me forever to find out how to get the last few ability points after I completed all the missions but after some digging I figured it out.
Theres two ways to get ability points. The first is from completing main missions and side missions. Keep in mind that Bureau Alerts don't give ability points. so make sure you've completed all of these.
The next way is by discovering hidden areas. Finding them awards 1 point each. After you've finished all missions you should have less than ten ability points remaining in order to complete the skill tree. This link gives a great guide on where to find these hidden areashttp://www.powerpyx.com/control-all-hidden-locations-guide/