Josef II tried to do just that, and failed. He wrote his own epitaph that said "Here lies Josef who failed in all he undertook". Now, Josef was a micromanager at the worst level, but maybe if Leopold II had lived longer/succeeded earlier and tried to implement such a plan (in a similar manner to how he pushed reforms through in Tuscany), and the French Revolution hadn't been going on, it might've been successful. Though I doubt it. Maybe if it had been done a whole lot earlier 16th-17th century perhaps. But I'm getting off topic for this thread. Don't wanna derail it.
You're not that far OT.
Your point that it would take generations rather than years is the key one. Thus Alsatians, though speaking a German dialect, had been French subjects since the Thirty years war, and had come to think of themselves as such. In the same way, if the Napoleonic Empire had lasted a century or two it is conceivable in theory that non-Francophone elements might have become reconciled to it.
In practice though, it is most unlikely that this would get a chance to happen. Nationalism was the rising force everywhere. Frex, in 1815 to all appearances Bohemia and Moravia were German. Czech nationalism was barely a glimmer on the horizon. By 1848, OTOH, it was rapidly emerging, despite the fact that the Czech lands had been Austrian for centuries, giving them a long common history with the other Austrian lands. Napoleon's Empire, by contrast, was just a collection of odds and ends with no common history or tradition, arbitrarily cobbled together at the whim of one man(and this well within the lifetime of most people alive in 1848), so much more vulnerable to nationalist forces as these arise over the next generation or so.