Cognitive Grammar (CG) views categories at a level of granularity that is below the views espoused in the current edition of Cognitive Construction Grammar (CCxG); instead of using prototypes, CG relies on an quasi-atomistic assemblage model for category formation. CCxG on the other hand could be seen as a more stochastic stab at the problem of category structure, since it is based on prototype effects. To me, these do not seem to be mutually exclusive foci; CG answers a lower level problem than CCxG. CCxG does not need that level of analysis because of the emphasis on generalization in construction use which exist at a higher level of concern.
Also, CG differs from CCxG in that CCxG looks at construal of meaning to be situation based and a matter of choice, CG, on the other hand, views construal as a fixed attribute of form. Consequently, CCxG may have a better view of semantics than CG since CCxG is not rigidly tied to the formalisms required by a reductionist model (even if it does maintain the claim that constructions are form-meaning pairings).
CG in this view, seems to be more focused on an association-based model to account for form-meaning pairings and CCxG seems to rely on construction generalizations to establish the meaning and frequency to confirm the form.