What are all of the ways to obtain upgrade points?
The two ways as far as I can tell: (After maxing my warlock subclasses)
1) Leveling up, you'll continue to earn them this way past 20 until you've filled out all the skills in a class.
2) Doing adventures that have upgrade points as a reward. If you've fully upgrading each subclass these rewards will change, usually into blue engrams in my experience.
3) If you do meditations and still need upgrade points you can get them from those.