The JP2KReader appears to have been enhanced over the past year to work somewhat without the Kakadu native libraries. However, when the code tries to get the GeoTIFF metadata, from the JP2, it won't even try if its not dealing with a Kakadu based image reader. That requirement isn't necessary since Sun specified with the metadata tree looks like for JP2: http://download.java.net/media/jai-imageio/javadoc/1.1/com/sun/media/imageio/plugins/jpeg2000/package-summary.html I am attaching a patch here that fixes this. It works correctly in my environment. I don't have a JP2 with GeoTiff headers I can share for testing and so there is no test.
My employer has relinquished copyright claims and I submitted the required form to Tyler Mitchell at OSGeo.
I would really appreciate this getting into v2.7.