Maybe just get rid of the bonus when shields are fully depleted? So a fully-depleted shield does not recharge any faster than a shield that got cut down to 1%. Shields are already very strong.
Make it so when a shield goes to 0%, shield strength slowly recovers at the same rate as if it had been taken down to 1%, and also that the shields don't provide any protection (and don't take any damage) until they recover to at least 25%.