its trail and error people... you open up the doors to complete freedom and customization. then watch what the people do and see what becomes the normal/most powerful/most sought after. THEN instead of nerfing those to be on par with the jobs no one wants to play... you look at how you can make up for the short falls of those weak jobs. AND YOU DONT DO THAT BY INCREASING THEIR POTENCY. you actually make changes to the abilities and make them more fun to play. like giving drg the chance to dodge while jumping (like ever freakin other FF in history) or giving the PLD the ability to raise in battle or actually push out decent heals while another healer is being raised (to take the safe slow route to ensure victory)... or making the war dps respectable enough for a 1 tank situation be a balls to the walls crazy kill fest that could just as easily find defeat (going the NOT safe route lol)
Just like all of the Final Fantasy's in the past... having a particular job in your team gives you both benefits and drawbacks (like using all drgs with dragon lances to defeat neo-shinryu or not being stupid and brining blms to the Omega MKII fight in FF3) the devs just needs to figure out how to have BOTH the benefits and drawbacks not outweigh each other in awesomeness.