Problems I'm seeing is like many things, it can be abused causing huge problems with the DF queues. Pausing to run to the restroom sounds ideal, but then again there are those who just pause it and take a nap, cook dinner, cut the grass, hoping that when they come back they can take pause off and have less of a wait time.
I see this as causing a big pile up in the queue as well. Even more so than it is now with the huge player base that FFXIV has. Players, jumping paused players queues, I am not sure this would work in theory, I think the way the queue is set up now it has it own limit cap. I don't want to see the limit cap to fill up with players on pause, sort of like when the Firmament Fate system filled and players would get locked out.