Just a thought, but you could work around this exploit by essentially having stun do 9 AP of transferable stun damage to the target. For this to work, ending your turn has to count as the unit having full AP again. This would mean that a stun against a unit with full AP works exactly as it does now – they skip their next turn. Similarly, a unit that decided to wait but still has full AP, would just skip that turn like they do now. However, if the unit has decided to wait but spent AP, then the amount of AP damage that remains after being deducted from their AP pool would transfer to the next turn. As a result, you can’t casually use the wait command as a buffer against stuns, because you’ll be hindering yourself in the turn that follows.
For example. A units spends 4 AP and waits. That unit then gets stunned. The turn they were about to receive is skipped and 4 AP is deducted from the AP pool of their next turn.
EDIT: Sleep deprived math error. Embarrassing.