Wow, this petition appears to replace the legislative process with one that permits the Commissioner, at will or whim, to make decisions that are regarded as law.  It also attempts to define the anadromous  fish habitat to every gully, ditch, culvert, etc. whether it has water or not , only if it could have water.  
Quite slyly, it seeks to exempt government AND native tribes from posting performance bonds.  (This bonding measure seems to be a major deterrent to financial investment of a large project). 
Yep, this looks like an anti-Pebble and anti every other large mine.  Large projects are grandfathered ...until their licences come up for renewal.. Or until any local jurisdiction initiates a new permit requirement, thereby invoking the petitioned process provisions.  
It appears that this petition has many, many provisions for application of "gothcha's" to any, large or small, development of any kind, in Alaska.