As we know, Napoleon defeated both these nations quite decisively. Prussia was saved by Russian intervention, while Austria was on its knees- longer campaign would surely allow Bonaparte to split Habsburg Empire.
Now we know that (in long terms) keeping these 2 countries proved to be bad decision. It culminated during Battle of Nations, when Napoleon has been defeated by (among others of course) these nations. So- what if Napoleon decides to split Habsburg Empire to smaller realms (most likely- Hungary-Croatia, Bohemia and Galicia going to Duchy of Warsaw), and doing same thing for Prussia? Apart from it, he could reinforce by their his only real ally during war- Poland. Thus directly challenging Russia of course...