It is revealed that Yami's Millennium Puzzle has the power to put souls back into their original bodies (he uses it to help Bakura.) If that's the case, why didn't he just do that with Yugi's grandpa when his soul was taken?
Yami Bakura uses a trap card called Just Desserts to inflict 500 damage to Yugi's life points for each monster he controls. If Bakura had simply waited for Yugi to summon an additional monster to the field instead of just wasting the trap card, he could have inflicted more life point damage and won the duel.