The NY Times actually noticed that it's taking rather a long time. This one is probably hung up in Corps/EPA disagreements about the practicability of various potential measures for determining jurisdiction.
EPA, being the stewards of the definition of "Waters of the United States," has an enormous stake here -- and since the definition of WOTUS applies across the entire range of EPA water programs, not just the Section 404 program, EPA's sense of ownership is broader and deeper than the Corps', and changes in jurisdiction are more consequential for the agency's overall reach. Corps Regulatory, by comparison, is one small office within an organization that is still miniscule -- both in personnel and in budget -- relative to the Department of Defense in which it sits.
On the other hand, on a practical day-to-day basis it is the Corps who goes out into the field every day and makes the 404 permit program work. By the numbers they have probably 10 times the field staff committed to running 404 that EPA does, in 38 Districts (as opposed to EPA's 10 regional offices). The daily grind of issuing permits and interfacing with the regulated community falls almost entirely on the Corps' shoulders. Although EPA has the ability to comment on whether the Corps has correctly applied the environmental criteria for permit issuance at 40 CFR 230.10(a-d), they do not have staff time available to comment on all permits. And at any rate the majority of permits are Nationwides, which other agencies do not comment on (except when the suite of NWP categories are approved every five years).
Last June's draft Jurisdictional Guidance gets high marks from me for trying hard to make the Kennedy concurrence make sense in the real world, but it does so by approaching the concept of "nexus" with a good deal of nuance and ecological sophistication. This could all translate into a lot of hard work -- very hard work -- on the part of the people who delineate wetlands and review the delineation reports for the purposes of establishing jurisdiction. My guess is that doing a full "Kennedy Waters" analysis for each delineation would require far, far more staff time than the Corps has. It could result in less overall protection as staff time gets concentrated on a few projects at the expense of others that get less scrutiny than they deserve.
So, ever thus: the Corps is always trying to give its field staff space to do their jobs well without being overwhelmed by impracticable directives from on high, while EPA is always trying to keep the integrity of WOTUS from being further eroded. Both worthy goals.