From what I can tell, it looks like they just assumed PLD+WHM for every fight as a design basis. Result is that mechanics are focused around one opponent smashing for huge damage, which goes right ahead and kills WAR outright. That would not be a character balance problem, per se; that would be an encounter design problem. PLD scales to damage, so PLD wins in high-damage situations. Up and make almost every fight the exact same design scenario -- throw big damage at one guy -- and PLD is going to be preferred for every single fight. Of course, at the same time, the current overall battle design has healers with way too much MP and healing for way too much. With healing as it is, WAR has a tough time making a meaningful difference with its drain. Even the 300% recovery on Inner Beast is nothing when your tank is getting hit for 1000 damage per second. To match the additional mitigation from Shield Oath alone in that scenario, Inner Beast would have to heal about 3500 HP if it goes off every 17.5 seconds. That would be comically overpowered and won't happen. PLD is going to be the preferred tank in most situations for mathematical reasons.
WAR has a few other disadvantages, namely stun and silence, but that's really secondary to the fact that WAR can't tank because of how much they increased healing amounts (roughly double over Phase III) and how encounters are designed.
