Two considerations following your thoughtful post. 
1) I think Congress consistently passes decisions to exec. agencies because “the devil is in the details.” Those agencies should have subject matter expertise & cannot act contrary to statute or in an arbitrary or capricious manner (as is typically left to courts to decide). On the other hand, Congress is basically limited only by the Constitution and their self-imposed rules. Congress is free to get as granular as it wants in defining WOTUS. But Congress has no subject matter expertise. A sort-of 'pick your poison.'
2) Beyond regulation, We The People permit ourselves to be taxed. Congress sets laws limiting how executive agencies spend our taxes. Whether you vote R or D, or agree with Mr. Pruitt on WOTUS or not, the editorial highlights how members of this administration are probably using tax funds improperly. Which is all the more frustrating following a “drain the swamp” campaign promise.