You're right to a certain extent, IMO it'll depend on how overextended this French Empire will be. I mean, certainly important cities like Milan or Rome wouldn't simply turn French within a century, but cities like Amsterdam and the Rhine-Ruhr area would probably be totally French within 2 or 3 generations of peaceful and progressive rule, as more people come to the cities not only from the surrounding areas, but from all over the empire.
It's important to put all the national awakening movements in the context of the social backlash of the Congress of Vienna. Depending on how this French Empire is seen by its subjects, French will probably still me seen as the "language of the revolution", what would be added to its natural role as supranational language par execellence. Also in this context nationalist movements will probably be promoted by the most reactionary parts of the conquered societies and, obviously, would not be as attractive to the lower classes as it was in OTL.
In OTL cities like Perpignan, Strasbourg and Nice (the birthplace of Garibaldi!) were almost completely francized during the late 19th century and early 20th century.
Realistically, I can see the Low Countries, the Rhineland, parts of Northern Italy and possibily Catalonia as a part of a functional Napoleonic Empire. IMHO If the empire manages to stay strong during the 19th century these areas could be as French as OTL Belgium before the Flemish Awakening.