This seems to be in the same vein as other topics on nationalism so I'll just rehash my points.
First, wrong culture's penalty in EU2 was very low. You got less manpower, but there was no stab penalty. So it was always worth it to eat up all of Catholic Italy as Catholic France for example. Wrong religon provinces were trickier, which I believe is accurate since the examples of bohemia and to a lesser extent the Ottoman empire besides, monarchs tended to ally themselves with one church or the other for tangible benefits, and religous tolerance was pretty low in general.
Secondly, core (or culture) switching to the dominant powerwas infrequent and when it did occur only seemed to happen after centuries. Wales,Scotland, and N. Ireland eventually became English cores after a century or so, but Ireland did not despite being dominanted for just as long. Corsica became a French core, Sicily did not become a Spanish one. It seems to me that the general rule was that most "foriegn" territory ruled by European monarchs never became as integrated as the "natural" provinces of the country.
Finally its true that Austria and the Ottomans did a good job holding onto diverse territories. But I do not think they did as good a job as a "native" ruler would have done. In EU2 the Austrians get just as much tax and manpower from Hungary as a Hungarian king would have. Its true that the Ottomans brought many skilled Greeks into there service for example, and made loads of the unbeliever tax, but does anyone believe that the Ottomans were able to rule Greece as effectively as a Greek king who could build a centralized state and ally with the patriach? Could the Ottomans ever control the Serbs as effectively as they controlled Turkish/muslim dominated provinces? In the sense that EU2 lets the Ottomans and Austrians seamlessly convert, tax, and recruit troops from province they had some trouble with EU2 is too liberal with state cultures/cores. Maybe this is needed for gamebalance reasons.