Historicity has a limit, even in eu2. I mean, look at the Timurids for example - no matter what, they will give up most of their land to "sucessor states". You must leave a gap between historicity, and fantasy.
About Austria inheriting Hungary/Bohemia/Burgundy, i dont see a problem about it. Do you think if they didnt in real life, Austria would be the dominant german state and the european power they became? And you cant compare the historical importance of the Austrian king inheriting Bohemia or the Spanish King being made Portuguese King as well, with the "Portuguese takeover of Kongo". I am from Portugal and i never ever heard such. While Filipe's II being made a Portuguese King is known everywhere (in Portugal), and even taugh in school.
If these events are to make the AI play historical, then, create a condition making them only for AIs.
Now to answer the main question... Which events i find bad for gameplay? Well, nearly all - no offense to the ones that made em, but the event file needs to be purged.
First of, Henry's captains. I dont consider it the worst event ever seen, nor does it harm the player, but why does the event ever exist (together with the ones that give you explorers)? The event(s) shouldnt exist, and these leaders should pump out at the acordingly date no matter what. I mean, come on, most explorers "required aid" from the monarchs, but that doesnt justify making events for only a bunch of leaders while the others got none.
Second of, events that force you into war with other countries like Malaca or most events regarding India. If we started doing events like these, we should make events for every puny war that hapened in the world during eu2's period. Again, if these events are meant to make the AI play historical, then, add a condition for only AIs.
Thirdly, event like vassalization of Kongo, Zanj and Ternate and so on. These events give these little minors freely as vassals to Portugal without Portugal moving an inch. And honestly, they arent really historical relevant to have been added. Yes, Austria inherits Bohemia and so on without moving an inch as well, but they were really important for history - who cares about a province minor that lays on the middle of nowhere and never contributed anything to mankind?
In other orders, the mod focus on too little minor details that arent really relevant, and then, forgets and fails to add really important things - where is, for example, the Portuguese age of Absolutism? The era where due to gold from Brazil, Portugal rivalized the "Sun King" of France?
And lastly, i dont mean to offend anyone - since i believe whoever made the events really put a lot of effort and time doing em.