In early 1997 a federal court invalidated that rule, and the Corps has appealed. Stay tuned for updates on this issue. Hopefully the former. In some cases you must notify the Corps in advance of your activity, in other cases you don't. Further changes to the NWP program are expected in late 1999.
Individual permits are more time consuming.
All 404 permits need a Section 401 water quality certification from the state. In California, even nationwide permits must go through the 401 process through the Regional Water Quality Control Boards. Local governments also get into the act in connection with the local land use approval process. You may also be able to design your project so as to minimize, or even eliminate, your 404 permitting hassles. There are a number of very hot issues in the wetlands arena at the moment.