The problem with that it would create resentment between different units. Soldiers would look down on the less physically fit, even if they had higher rank. Also all soldiers need to be able to pick up arms and fight. The PT standards are the minium fitness level. I would hate to see us lower it even more.
There are disadvantages, but different MOSs already look down on others. Of course, the minimum standard would be the minimum to fight, but if you want to get into infantry, better train some more. There are already extra tests to get into certain outfits, like the Special Forces, I'm just extending the idea.