The EPA under Obama disregarded what their charge is, which is to control a process that is in place, through current regulations and laws, and allow the process of gaining permits to proceed. Instead, the Obama EPA circumvented the process to fit their own agenda, which was to stop the Pebble Mine project. As citizens, we should all be up  in arms with what they did. What Pruitt is doing is to allow the process to proceed and if Pebble gets turned down because they do not comply, then so be it. If they are approved, it will be due to their following the permit process and gaining their permits' approval. This is the way it should be: Obama's EPA chose favorites, while Trump's EPA allows the established permit system to play out, with an up or down decision as the result. 
This decision is excellent for not just Alaska, but for the entire US.