Permits are required for a…

Permits are required for a reason and there will be much more waste of resources and money in the case where a project is begun and a permit is later not granted. Then the work that had already started would be a waste of time and resources as well as would have already disrupted the ecosystem that was already in danger (hence not receiving the permit).
The only reason a permit should take so long to grant is if there is potential reason to not grant it. If acquiring a permit is so difficult, there should be work going into making this process more efficient instead of this kind of work that will only create loopholes and cause waste and destruction to our endangered species.