I'm level 50, but I only have 2 points to spend and 2 abilities left to unlock. Side quests only give XP so what now? Level 50 is the max level so XP from quests do nothing. In fact, I think I've completed all quests now. How am I supposed to unlock the other skills if I can't get any more Skill Points from leveling up?
The main quests as well as the Hunter Trials will award you Skill Points. If I remember correctly, main quests usually give you a Skill Point as a reward. Getting Blazing Suns on all 3 Hunter Trials at a Hunter Trial area will also award you a Skill Point. Additionally, completing Cauldrons and climbing Tallnecks will reward you Skill Points. If you haven't done all of these, you definitely should. From experience, I capped out my Skills by the mid-40s and was still receiving Skill Points from main quests and level ups, despite having nothing to spend them on.
By the end of the game, completing Hunter Trials and Main Quests should award you way more than the required number of Skill Points required to unlock all skills.
Collecting all the metal flowers, vantage points, vessels and banuk figures each gives tons of skill points! At the time I found the last metal flower I had 5 Skill Points saved up. It jumped to 11 when I earned the flower trophy! They also jumped when I got the last ancient vessel, etc. Easiest way is to buy the maps locating the collectibles and bounce around campfire to campfire with Golden Fast Pack until you've got them all. I'm only at level 43 and I only have one skill left to unlock.