The medical system is structured in such a rigid way that the only way they can support transition is if they define it as a condition that they can treat - this is one of the downsides of allopathic, menu-driven medicine.
At least the WPATH is progressive, in that each time a new one comes out they take a step further away from defining trans as an illness and move towards recognising dysphoria as a response to a condition, not a condition in itself. I think a lot of the fault lies with the underlying medical model that WPATH has to respond to, not with WPATH itself.
And in the end, most people's problems with the medical profession are problems caused by the personalities and prejudices of individual practitioners, rather than the system as a whole. Good, progressive doctors and psychiatrists (and they certainly exist) recognise their role as that of supporting people in their transition, rather than exploiting their own powerful position to shore up their egos by setting up barriers. The GIC I attend in Devon, for example, has a much more progressive reputation than the dreaded Charing Cross one in London, and that's all down to the views of the people running it - after all, they're operating under the same healthcare rules, they just interpret them differently.