Right now in the system we got a character can actually cap out once all their stats are maxed, once this happens, prestige with this character can be leveled up (Think like Badass ranks from Borderlands, whereas benefits are small per rank, but infinite), another kind of reward would be to unlock a secondary class for the character.

The prestige ranks up could be things that does not unbalance the game in term of efficiency, it can be XP boost ranks up for characters that haven't capped their levels yet, Passive XP earned for every team members on your roster after every mission, retraining tokens (So you can choose a different class with an old character if you prefer a new one but are stuck with the old one), Customization tokens (Freed an hostage but doesn't look the way you want? Take one of these), Specialization tokens (Reset your character back to level 0, but with a permanent bonus that you cannot have by any other means)

Anyway you get the idea, infinite progression is a very valuable thing in a game in my view.

About cooldowns, i would like to suggest instead an energy bar (Default being 100 and can be improved with gear), whereas skills are no longer linked with cooldown by turn, but rather by the energy cost they use, and energy regen per turn (Which can also be improved with gear), this system would give you a lot more flexibility rather than fixed cooldowns.