Here's a thought. Have merits set for individual jobs instead of all at once.

For example, you have a player named Samwell. He plays White Mage, Paladin and Monk. When he he changes to White Mage, his merits change to where his MP, eminity down, staff and club skills (as well as the merit weapon skills) are maxed. He changes to Monk and his HP, H2H and club skills (again, as well as the merit weapon skills) are maxed. He changes to Paladin and his eminity up is maxed, his HP/MP are equaly merited, and his Sword, Club, and Staff skills (as well as WS) are maxed.