I just don't understand why he didn't. The Austrians were ever a thorn in the side of the French and were one of the premier powers of Europe. Napoleon defeated them time and again, why didn't dismantle their empire completely?
It's not like it was completely without precedent. Napoleon didn't mind toppling monarchs and governments and replacing them with whatever suited him. He also had no problem reviving old countries and creating new ones such as the Duchy of Warsaw and the Confederation of the Rhine.
Sure there were more than enough restive minorities within the Austrian Empire that had previous histories of sovereignty. The Czechs, the Hungarians and the Serbs could all have been established as independent (albeit perpetually tied to France) nations along the lines of the Duchy of Warsaw.
The benefit of this would be two fold; firstly they would have provided plenty of troops. The Poles proved to be loyal supporters of Napoleon and made a significant military contribution to his campaigns. I'd imagine that other 'liberated' countries would prove just as supportive.
Secondly and probably most importantly, the loss of their empire would cripple the Austrians and severely deplete their available manpower, making it extremely unlikely that they would be capable of significantly challenging Napoleon.
Now chances are even if Napoleon had done this he would still have lost in the long run if he went ahead with his ill advised invasion of Russia. However, in general, crippling Austria could only have benefited France, so I just don't understand why he didn't do it.