All good thoughts. There were Muslim revolts in the Ottoman Empire, usually against reforms or increased taxes, not the Empire in itself; that was also behind all the Christian revolts too, BTW.
If you think about it, the Serbs revolted against local Janissaries on behalf of the Sultan, Bosnia over a bad harvest and taxes, the Albanians because the Treaty of Berlin mandated Albanian lands go to Montenegro, and Bulgaria did absolutely nothing whatsoever to "liberate" itself, and Bulgarian nationalism, such as it was, was resistance to Greek domination of the Orthodox millet.
I don't disagree that in general the level of support for a particular nationalism wasn't all that high. Most of the revolts were not based on nationalist reasons, they were much more about local problems. Also, the differences between the various Orthodox Slavs were largely creations of state power structures, not actual differences between various groups per se.
That being said, I think that if you have a greater amount of central Ottoman control, and thus I would think greater economic development of the Balkans, then you are going to create a class of Orthodox Slav intellectuals. These intellectuals are going to take their cues from Western Europe, where nationalism has become the organizing principle of the state (thus nation-state). This rise of nationalist intellectuals is going to make these people aware of the population differences, and the problems that they would face in a revolt. This, plus the already present religious-ethnic differences, I think, would push these Slavic intellectuals to want to reconcile Serbo-Croatian and Bulgarian, and push towards the creation of a single Yugoslav identity. This identity, rooted in Orthodox slavism, would find an easy sponsor in the Russian Empire, and I think that those intellectuals would also give the Yugoslavic identity traction in the West. The reconciliation of Bulgarian and Serbo-Croatian, and thus the linking of a Yugoslavic identity to a common language, the basic requirement in Western Europe for nationalism.
Only Greece revolted for "higher" reasons, and that was an attempt to reconstitute the Byzantine Empire - and all these needed large-scale external support to succeed.
It's not just that the number of Muslims were high, but where they were high - along the Danube and in Bosnia, plus Albania and Epirus. The Christian areas were in the middle of the peninsula, and just north of Greece. I have a population map of the empire c. 1875, broken down by subprovince - I'll have to post it.
As OTL history proved, committed campaigns of ethnic cleansing can change the ethnic makeup of regions.
If the empire were stronger, would other powers be able to interfere so much? Hungary already has a lot of Slavs in it - isn't it in her best interests NOT to have any Slavic statelets on its borders? Will a Hungary-free Hapsburg state become much more Germany-focused?
Hungary and Austria I wouldn't expect to do much in the way of expanding into the Balkans. Hungary may want to extend her border directly east, along the Danube River, to gain control of the mouth of the Danube. The power that I think would have the most interest in the Balkans would be the Russians. If the development of Slavic nationalism happens as I have it above then I think the Russians would be outrageously happy to support the Yugoslav's nationalist aspirations.
Prior to the Treaty of Berlin, "nationalism" in the Western mind was limited - in the sense that only a handful of nations were considered large enough to merit nation states... it was that treaty that was the triumph of the national model vs. the dynastic. Would more stable Ottoman and Hapsburg states make things move in a different direction? Nationalism today has largely run its course - Islamism is largely a reaction against it, as is the EU. If these empires had survived longer could Universalism gained a second wind?
I don't think so. The Ottomans may have had more central control and better armed forces, but the Russians are a large and motivated country. If they face stronger resistance from the Ottomans, this could end up spurring Russian reforms that could end up hurting the Ottomans rather badly.
I really don't believe that Universal Empires were in the cards any longer. That doesn't mean however that the Ottoman Empire can't remain a power, and maintain its Imperial borders. If you have a transition to Turkish nationalism within the Ottoman Empire, then you can have Anatolia as the Turkish "metropolitan" and the rest of the Empire as the colonial territory. If you are able to create a plastic enough Turkish identity that embraces the Balkan Muslims (something that I think should be doable) then you can definitely maintain the Empire. In Arabia, there was little nationalist feelings, even during WWI. I would say that anti-colonialism finally gave Arab nationalism its big kick in the pants. With Muslim identifying as Turks in the Balkans, and the rest of the Empire quiet due to lack of nationalist evolution (though perhaps with the increase in central control you also create greater Arab national feeling ala the situation that I have developing in the Balkans) then you could have an enduring Ottoman (Turkish) Empire
In the case of the Ottomans, the empire isn't just the Balkans. Add in the rest of it and Bulgarians, for instance, are a small minority in a little corner of a large state. Are the more likely to leave a powerful state than say, the Basques?
Because of the potential to make common cause with other Orthodox Slavs, indeed I would argue the imperitive that that they make common cause with the other slavs, the Bulgarians as such would not be acting alone. They would be acting as a part of a larger national community, the Yugoslavs, a national community that the Basques never had access to.
Hungary-Bohemia is certainly an interesting idea, and they were after all just recently dynastically related...
But this state is going to include an awful lot of Slavs, including all the Czechs and Slovaks, and it's position is going to keep it really busy in Germany, with the Hapsburgs, the Poles, and eventually Russia. I'm not really seeing where their interests collide with the Ottomans'.
I think that with the Calvinist base of the monarchy, and the shared threats from both Germany and the Ottoman Empire, would probably create some kind of shared national identity, though I'm not really sure. You could end up with a sort of situation like you have with the Austrian and Magyars in the latter part of the 19th century, where the Czechs and Magyars need each other in order to maintain the kind of influence they feel they need. I would throw in a long-lived dynasty that can command the respect and legitimacy necessary to maintain this dual monarchy.
With respect to the Austrian Hapsburgs, I don't really want to hazard a guess. I would say that there are going to be some seriously good reasons for the Hapsburgs to be able to establish more control over Germany, and just as many for them to fail to do so.
I think that Poland would probably end up surviving, maybe with a Hapsburg on the throne (hey if they don't get Bohemia and Hungary, they're going to need to gain some more thrones).
What do you think would happen to Croatia? Does it remain with Hungary?
That's tough. I think that the Croatians would probably revolt against the Hungarians and get Austrian protection. The shared threats of Hungary and the Ottomans, combined with the shared Catholicism, should keep Croatia a loyal part of the Hapsburg Empire (as it was OTL).