Well, something somewhat similar to the structure of France before Louis XIV would be pleased. I mean quasi-federation of duchies/lands (each with particular customs, laws, culture, language etc.) under the dominance of one capital region, which in our scenario would be the hereditary domain of our emperors. Maybe with a greater role of federal institutions such as Reichstag, Reichskammergericht and so on. Maybe such structure should be based more on imperial circles which would contain lower units, rather than on messy collection of duchies, counties, free cities, bishoprics etc. known from the OTL. About the emperor's power - it surely wouldn't be absolutist. Cliques and alliances of cities and aristocracy will moderate the emperor's actions and try to preserve status quo. That's of course the ideal structure and I know that reforming the country from it's decentralized form would be a bit harsh 
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