I understand the need to balance Innate Ranged Attack against people using conventional ranged weaponry, but is the ability to make a simple ranged attack something that needs to be use-limited?
I think so, yes. It does need to be limited, at least in a manner that prevents it from being overly abused. Perhaps one method, beyond the usage of power points as described above, would be to allow it to continue to be used AFTER the character runs out of power points, and having it cost the character a number of hit points equal to the Base Damage of the ability.
for example, using a basic Innate Ranged Attack - this shoots a bolt of chi energy at the foe and does 6 points of Base Damage. Character has a Willpower stat of 19. This allows him 6 bolts normally before he needs to rest. Once he has used the 6th bolt, he has 1 PP left, but that cannot be used since there aren't enough. So, any further attempts to use the Chi Bolt will incur a -2 penalty on that usage (i.e. attack roll) and it does 6 points of damage to the character.
This would allow him to continue using it, but it would have its costs as well, and the player would have to balance that cost against the usefulness of the ability...