To avoid making Paladins and other horse riding units seem pointless. Pegasus and Wyverns without weakness remove the point of ground cavalry.
Not really... Having the shields didn't make Paladins and such useless in past games. Especially not when there was only one of those particular items in the game. Sumia still has a defense issue. Plus most people use more than one flyer, anyway. So you gotta choose who to give the shield to.
Besides, the shield in the pass only protected again arrows.