Maybe include a way for the characters to learn their abilities from a certain NPC in the form of a task that would grant you an ability at the end, instead of straight out getting abilites after repetition of some similar ability.
Ex. There was talk about flying being a separate level-up skill in a different thread. Level one, every flyer starts out like unflyable Petrie. Then, at level 2 or something, instead of immediately getting the ability to glide, or being able to allot "points" to gliding, you could talk to Guido, who will teach you how to glide if you do a task for him and if your level is high enough. Then some more levels later Petrie or maybe even Pterano can teach you how to fly.
Also, would treestars be a form of payment/currency for completing tasks?
Interesting that you brought up those ideas, as I have thought of using that system for learning abilities as well.
The system I'm picturing for abilities in our game is basically what you described there, NaNaNa. I'm thinking:
There could be some abilities that are learned automatically when you reach a certain level. There would not be very many of these.
Most abilities would be taught to you by an NPC, either as a reward for completing some task or some other reason. I'm also picturing some tasks involving learning a new skill from an NPC then being expected to apply the skill to complete the task that NPC gives you. ( "Here, I'll show you how to do this so now you can go do something for me!", basically)
Some abilities or ways to improve or "specialize" your abilities could be earned by spending points that you gain when you level up.
As for treestars being a currency, I thought about it but the decision on that was, * our game will not have a currency system because it seemed too "human" and not "LBT-like" *. Some tasks may involve giving and receiving but that's the extent of currency in our game.