So basically, IOTL the Habsburgs rolled natural 20s on most of their marriage alliances in the early 16th century - the Catholic Monarchs didn't have a surviving son to succeed them, and the line was passed through Juana rather than her elder siblings who predeceased their parents and left no surviving issue. Then on top of that Louis II, last of the Bohemian branch of the Jagiellons, got himself killed at Mohacs, allowing Charles V's brother Ferdinand to step in and claim Bohemia and Hungary based on being the husband of Louis' sister.
So let's say Louis II doesn't get himself killed, or at the very least gets his wife Mary with a son. How does this affect the Habsburg outlook going forward?
There's what happens to the Habsburg, and then there's what happens the Hungarian-Bohemian personal union under the Hungarian branch of the Jagiellons.
Can the the Hungarians hold out in a combination of most or part of their country, plus Bohemia, or will the Ottomans conquer/vassalize all of Hungary?
Will we see an Ottoman siege, or conquest, of Prague, instead of one of Vienna, due to the Ottomans pursuing Jagiellonian forces rather than Habsburg ones?
Without merging with the Habsburg, will the Hungarians ever regain everything they ever may lose from the Turks, like Croatia, southeastern Hungary, Banat, Transylvania, back from the Turks?
Back in the Hungary-Bohemia-less Habsburg lands, does the lack of Hungary and Bohemia in his domains relieve Charles the V of enough of a burden that he chooses not to retire, or not to split his lands, keeping Habsburg lands of Spain and Austria undivided?
Or does he split them? If he does split them, either at his retirement like OTL, or at his death, does he apportion anything else (likely in the HRE) to Ferdinand rather than Philipp, since Ferdinand does not possess title to Bohemia and Hungary?
With Hungary and Bohemia remaining Jagiellonian and not Habsburg, is the Counter-Reformation any less intensely successful there, and does Protestantism remain stronger?
How are wars of religion changed in the absence of a Habsburg Bohemia?