GlueGen does its best to emit proper names for arguments. It will emit the correct name if the args are named in the function prototype. E.g., the Java/JNI equivalents for
GLAPI void APIENTRY glSecondaryColor3bEXT (GLbyte, GLbyte, GLbyte);
Will use the arg0...argN names, but the emitted equivalents for
GLAPI void APIENTRY glSecondaryColor3bEXT (GLbyte red, GLbyte green, GLbyte blue);
The easiest and most correct way to get properly named functions emitted is to add the correct names to the prototypes in gl.h/glext.h/glxext.h/etc. The reason I didn't do this the first time around was (besides the obvious gruntwork involved) because I wanted to make it easy to update JOGL when a new glext.h header was released at the extension registry page:http://oss.sgi.com/projects/ogl-sample/registry/index.html
Unfortunately, though those are the "official" OpenGL headers, they don't have argument names in them. It would be nice if someone updated those headers with the correct names and had the ARB re-post them.
Otherwise you're welcome to insert the correct argument names into JOGL's stub versions of the GL headers, and donate them back to the JOGL source tree.