Story related Spoiler incoming>
Spoiler:  Show
I'd like to point out that at the end of the story Pac Katari becomes enemies with Americans and you are unable to use the 'Rebels back-up' skills.
Once you complete the game I think it should stay that way.


1. Non of the Rebel skills are essential to the ghosts and game-play. But they are nice to have.
2. If you do a side mission, you automatically get to use corresponding Rebel skill at max-tier. The number of times you complete a side mission is the number of times you can use that skill. Eg. If I've completed the Mortar side mission 4 times, I can use that rebel skill 4 times.

Also freeing rebels from cages should add to the number of rebels that join you during a fight.
Right now I see no incentive to free the rebels from cages.

Basically once I've completed upgrading all rebel skills, I see no reason to replay the side missions.
I know this isn't an RPG, but the skills tree and unlocking weapons already has a "unlock/progression" system implemented. And since the rebel skills aren't essential but are nice to have, it's okay to have them disabled unless you keep helping them. And it ties in with the story as well.