When your trying to capture Palkia, DON'T USE YOUR MASTER BALL ON IT! use dusk ball because it is a dark place so dusk ball does twice as good as a great ball does. You should also make sure you have a pokemon with thunder wave with you. Also have a high leveled pokemon with false swipe, or use pokemon who could bring it's health down and not kill it. Then afterwards, you could save your Master Ball on Mesprit or Cresselia.