Honestly, the only good I see from not upgrading to the implied job is that you get to equip ten cross-class abilities (at level 50) instead of five, and you can choose cross class skills from any class instead of two.

Example: MNK can only pull up to five abilities from MRD and/or LNC. PUG can pull ten abilities from any combat class so long as it is a skill that can be cross classed. However, it will lose the five specific MNK abilities.

For MNK, that would mean loosing our gap closer (Shoulder Tackle), Fist of Fire (our Bread and Butter +5% damage buff), and Dragon Kick (10% blunt resistance debuff). RockBreaker and One Ilm Punch are more situational things.

In return, you get.... Raging Strikes from ARC? A CD damage booster with a pretty long reload.

Granted - that is just for MNK. Others might see a greater benefit. Won't go into the stat boosts associated with equipping a job stone.