In a foot note to his introduction to TJ Habermas attributes his difference with Apel to the theme of 'weak' naturalism. Here is the original note:
"K.-O. Apel has pursued [epistemological project] more consistently since his program of a 'transformation of philosophy" to this day continue to align itself with a Kantian transcendental philosophy. The deeper source of our difference . . . I attribute to my opting for a "weak" naturalism." (TJ: 294 n. 10.).