Not something I think is better necessarily, just a fun alternative. What if, instead of just regenning paintballs whenever, there is no paintball regen, but instead, /keepInventory is turned off. Any maybe if you reach the other team's spawn you get an automatic full set of 64 whenever you touch it.
EDIT: The full ammo thing at enemy spawn wouldn't actually be a thing for CTF, btw - just team deathmatch.
EDIT: The full ammo thing at enemy spawn wouldn't actually be a thing for CTF, btw - just team deathmatch.