To illustrate this with a real-world example of maternal succession I have turned to a bookmarks mod to select Queen Isabelle II of Jerusalem. Do not come at me, this is not a mod-related issue. You can reproduce it in the vanilla game.
Now, Isabelle II inherited her throne from her mother, Maria. In CK2, as well as in history, Isabelle II's heir was her aunt Alice, the eldest of Maria's younger half-sisters.
In CK2, as well as she was in history, Alice is followed in the line of succession by further half-sisters. All of them are the children of Queen Isabelle I, but by different fathers.
But in CK3 the heir to Isabelle II is her father, Jean de Brienne, who has no claim to the kingdom. This is because maternal relatives are barred from inheriting in CK3.
In fact, Alice could not be her half-sister Maria's heir either: although their claim to Jerusalem comes from their shared mother, Isabelle I, the half-sisters have different fathers and only paternal relatives can inherit in CK3. Of course, in CK2 Alice is Maria's heir before Isabelle II is born. We can see this in another example, Brittany. Duchess Alix was the daughter and successor of Duchess Constance. Constance had had children by two husbands. Alix's heir in CK2 is her older maternal half-sister.
But in CK3 Alix's heir is her younger full sister instead. Indeed, if Alix's father were to have a son by another wife, this half-brother would be the heir despite having no connection to the previous dukes of Brittany!
Back to Jerusalem now. Some may suggest that this is the result of male-preference succession. It is not and it should not be. We had male-preference succession in history and in CK2 and maternal relatives still inherited what they were supposed to inherit. Alice's descendants inherited the kingdom after Isabelle II's line died out. But for the sake of the argument I gave Jerusalem equal succession. Let's see what happens.
The heir to Isabelle II is still her father, followed by an irrelevant paternal cousin. But interestingly her maternal aunts now appear in the line of succession, although behind the entire (dynastically irrelevant) paternal family. This gives me hope that this is something that Paradox can address.
This has been a major grievance of mine for years. I hope it can be fixed. Cheers!