I think a big part of the problem is that vassalage in EUIV is painfully simplistic, ridiculously powerful and has no basis in history. Which, really, is a fair criticism of EUIV as a whole, but vassalage is an especially egregious example.
What is vassalage meant to represent? A territory being nominally allowed to retain its independence while an overlord takes over foreign affairs, à la the princely states in the British Raj? But how often did that happen in history, and why are they automatically called to war? A feudal relationship between liege and subject, as in the case between France and its various duchies? But after just ten years the vassal can be directly integrated into the realm without complaint, and at any rate we have the "nobles" estate and crownland. A frontier client state like Napoleon set up in Germany and Italy? But we have a client state mechanic, and no evidence that they got cheerfully re-absorbed (quite the opposite, they were set up because absorbing entire other countries is incredibly hard). A suborned trading partner economically controlled by a commercial hegemon? But we already have a “share trade power” mechanic, and trade leagues. A tributary that retains its independence in exchange for protection payments? But we have weird lopsided tributaries for that. A subsidiary inherited possession of a monarch? No, for some reason that’s a substantially different thing called a personal union. A smaller polity in federation with a more powerful one? No, the only way we reflect that is with... I guess alliances.
On top of that, various actual vassal relationships aren’t reflected—where is the Tatar yoke, for instance? The complex relationship between the Commonwealth and its Cossack territories? The long, long efforts of the French king to centralise power in his realm? The minor powers in federation under the Papacy? Nowhere, because the bland, one-size-fits-literally-nobody vassalage mechanic doesn’t reflect anything in history. It's just a weird, flavourless, super-powerful mechanic based on nothing.
In my opinion it’s the single worst mechanic in all of EUIV because it affects everyone in every game regardless of skill level or playstyle, and it’s just so completely senseless.
Vassalage should be redesigned as a combination of estates and Victoria 2’s reform system.
Using a combination of factors—how much bigger than theirs is your army? How are your relations? Do you have high trust? How are your other vassals being treated? Do you have the same religion? Are you the same dynasty? Are there other countries with high relations who might protect them in the event of an outbreak of war between them and you?—you could make reforms (or policy changes, or whatever) in your handling of each vassal in a number of different categories: tax policy, levying (do they contribute nothing, contribute manpower, let you recruit on their territory, contribute just ships, or get forced to join wars?), government, foreign policy (can they declare external wars like a tributary state? Will you protect them if they get attacked?), trade, and so on. Annexation should be the final step in that substantial process, and shouldn’t come (except in extreme cases) without serious resistance. Perhaps each reform could have an administration cost associated that weighs on your governing capacity, and/or below a certain level of administration cost the vassal doesn’t take up a relations slot... Maybe you could force reforms at a cost of potentially seeing armed resistance...
That would allow us to abandon the various kinds of subjects (almost) completely, replaced with a far more flexible and realistic system that could recreate all those relationships and more with the right combination of rights, privileges and demands. It would also enable a far deeper and more realistic level of engagement: instead of a laughably simplistic "liberty desire" and a binary support independence yes/no we could have a rule something like succession wars where, say, a France with relations above +75 with Bar gets a special, no-malus-for-saying-no call to arms when Bar declares a "Revolt" war against Provence demanding a HRE-style "roll back the last reform" in the peace deal. We could even see actual loyalty competitions for feudal vassals, so that Aragon and Castile have to constantly maintain the diplomatic arms race to win over and then placate Navarre.
This would open up a whole new scope of game as well, because it would broaden the "vassal" or "subject" mechanic to embrace a far greater swathe of potential tags. The Crown of Aragon could have its crownlands in the Kingdom of Aragon, vassals with very limited rights and privileges in the Kingdom of Valencia and Principality of Catalonia, and a vassal with very high privileges in Sicily, say. If we were really ambitious the 'nobility' estate could be virtually replaced by a robust subject system. What's more, it would finally enable coherent, engaging civil wars.
To get back to the subject of the thread: yes, the Crimean event as it stands is absurd. As others have noted, though, it's also historical. The problem isn't the event, it's the design of the game. If instead the event made Crimea a "subject" of the Ottomans with absolutely every reform toward freedom except something to do with the Ottomans picking their ruler, we wouldn't have this problem. Ottomans would be able to annex Crimea eventually, after a long and expensive process of manual, bit-by-bit, fighting-every-step-of-the-way integration... Or Crimea might just kind of potter along as a loosely controlled technically-subject, or spin off completely.
