Oh my. First lets first get some facts straight.
Austria, as an empire, didn't exist but for the last 16 years of EU4 timeframe. And the game models this perfectly. Once the HRE gets disbanded, Austria can finally stop being a "Grand Duchy" and click the "upgrade to Empire" button.
Hungary and Bohemia, two of the constituent parts of the Austrian Empire, were separate Kingdoms with separate crowns. The sheer number of cultures and languages in Austrian Empire made it improbable and impossible for the Austrian Empire to remain as it was originally planned. "The Compromise" that resulted in Austria-Hungary wasn't really a downgrade, as far as internal administration was concerned - it actually made it stronger.
I'm actually *for* Austria-Hungary being a formable country in EU4, with a new idea set that is better suited to a post-HRE world.
Considering Austria-Bohemia-Hungary managed to hold its own against France, Ottomans and Prussia/Germany for several centuries, especially considering all the difficulties of running a multiethnic empire, I think its fair to say that it did pretty well.