In the event of Philip only having daughters, Eleanor would inherit Burgundy upon his death. Eleanor would be heir to Joanna’s thrones and the most sought after bride in Europe. Eleanor would also be heir to her grandfather Maximilian’s Austrian possessions. Maximilian would likely seek to split his inheritance between his other granddaughters but Eleanor may refuse to renounce her succession rights to his lands in TTL. A marriage to John III would be the most logical choice for Eleanor.
If Eleanor, much like Charles, is unwilling to divide her inheritance amongst her sisters, is it possible that after marrying to John III and producing issue she finally divides the Iberian kingdoms? I mean, a personal union in which we have "Habsburg Dominions > Portugal" would lead to mass dissatisfaction, mainly from high Portuguese nobles such as the dukes of Braganza. This seems to be a great timeline, but I'd rather work it out in another topic.
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Back to the main "The Great Habsburg Sausage Party" Timeline, I enlisted superficially the possessions held by the Habsburg crown around OTL 1550's, and if it wasn't for damn laws of absolute-undeniable-land-concentrating-male-primogeniture, there would be enough places to be ruled by different sovereigns.
As follows:
The Crown of Castille:
1. Castille proper
Not much to say about it, the central-western section of Iberian peninsula (except, obviously, for Portugal) including also the lands of the former Emirate of Granada.
2. The Overseas Empire
There were the Vicerroyalties of New Spain, Peru, New Granada, Capitaincy of Chile, The Spanish East Indies and more... Any chance of turning those territories into hereditary vicerroalties governed by an European Habsburg prince (or maybe princes)?
The Crown of Aragon:
3. Aragon-Catalonia-Valencia-Balearic Islands proper
Self-explanatory.
4. Duchy of Milan
Actually the Duchy of Milan belonged to the already unified crown of Spain after the fall of the Sforzas OTL.
5. Kingdom of Sardinia
Eventually, OTL, would become an independent sovereign kingdom united to the Duchy of Savoy. What would be effects of granting Sardinia an earlier independence (under the house of Habsburg)?
6. Kingdom of the Sicilies (Naples and Trinacria)
Would also become independent, but under the Bourbons. Same question as above.
7. Southern Navarre
Could have its north-Pyrenees area conquered by force or maybe by another traditional diplomatic marriage. Or maybe everyone keeps okay with this, after all it's the largest part of the Navarrese territory.
The Crown of Burgundy:
8. The Seven Dutch Provinces
The division between Northern/Protestant and Southern/Catholic Netherlands would only strictly make sense in the context of the Dutch Revolt, but implying that as OTL it happens, there wouldn't be any chances of maybe keeping a Habsburg heir in power, conciliating the Protestant interests or perhaps offering a hypothetical daughter to William the Silent to keep the dinasty alive? Although not properly Habsburgs according to agnatic traditions, at least this latter setting would prevent a greater severance between the Dutch and the Spanish/Austrian.
9. Southern Catholic Netherlands and Luxembourg
Again self-explanatory. Maybe they start calling it "Belgium" centuries earlier.
10. The Franche-Comté
Any chance of Habsburgs preventing its slow-but-effective annexation by France? Butterflies (and LSD): an unification between Lorraine and the Franche-Comté? Oh wow, very, very far-fetched...
The Crown of Austria:
11. Austria Proper (Lower and Upper Austria)
The headquarters of the germanic Habsburgs and the german crown. Not much to say about it, besides that it's the most important area of Austria at the time.
12. Inner Austria (Styria, Carinthia and Carniola)
Another traditional appanage given to the non-first-borns.
13. Tyrol and Further Austria
The most irrelevant of all, but its proximity to the northern Italian duchies could lead to interesting alternative settings.
What can we do with all this now? Seriously leaving it all to one or at most two monarchs? Please add information and correct me if I'm wrong about something!