The permit process is very specific to where you live and the individual regulator(s) involved. How you approach the permit makes a huge difference from the first phone call.
Jersey, if you were confrontational or put the regulator on the defensive, good luck because you'll need it. Some areas (watersheds) have unwritten policies like "no net loss of wetlands" or maybe "no more ponds". The regulators may not not tell you about these internal mandates.
In Michigan there is a joint application for all environmental permits that goes to the MDEQ and is copied directly to USACE. I've designed gravel mines, lakes and ponds in wetlands and uplands and have never had to deal directly with USACE. I don't get involved with dams.
There is an art to the process but if your local guy is a jerk or having a bad day you better figure out a way around it, hire an attorney, consultant, call your congressman, move, or cancel the project. The environmental regulations are written so that regulators have a wide discretion and can basically turn down a project without reason. Do not put them on the defensive. If you have the type of personality that will come off as aggressive or combative, you'd better hire a professional from the start.
The major reason that I contacted the universities for a research program at my place (see post below) was to eliminate the arbitrary negative interpretation on wetland conversions by showing that open water environments and creation of upland edges is a beneficial part of a wetland complex. If the study is completed, hopefully we'll have documented research that shows benefits. I think that it also helped to leverage approval of the new permit that we needed to complete the project.
