I think cores vanishing is a good thing. There should definitely be a time limit to how late in the game you can bring the freaking minors back. Not to mention of course that the minors set-up was ridiculously unbalanced (France can be broken into a gazillion piece, but Castille and England can at best lose a peripheral piece or two).
It was cheese, and much as I love cheese, I'm glad this cheese is gone.
It still feels like the core disappearance should at least depend on the culture. As long as Galicia remains Galician and Brittany remains Breton, that is. Using the game-speak to refer to the real life, Cornwall and many of the Occitan minors (Toulouse, Provence...) did lose their cores as of 21st century (minimal to no national identity apart from UK/France) but Galicia or Brittany cores do seem to be still there. Not to mention those like Catalunya or Quebec, after a long time under Spanish/British rules.
And while it's cheezy, dissolving countries into minors did happen historically against the Austro-Hungarian empire (where they didn't share AH's primary culture, Austrian), while the German minors did lose their cores (Cultural union).
I don't mind culturally assimilated cores disappearing. I actually used it for my advantage (partially culture-converting Greece so the Byantium cores disappear in those provinces, and then releasing the remaining Byzantium to return cores back to them from the Ottomans...) But as long as the culture didn't change, it just feels strange that the cores vanish.
And yeah, it is unbalanced, and it's a pain to recover Iberian territory as Granada because of that very reason. (Well, in this case I know it's meant to be hard) But this cheeze was probably the only thing a player could use to smack down France because France itself is very unbalanced. Destroy their whole army, siege everything and crank up their WE to max, and they recover as if nothing happened. I don't think people will be upset about this change as long as there is a viable way to curve down some of the largest blobs in the late game.
I personally have no idea how to do this, but there should be a way to at least weaken one of your rivals enough even if the game wants to respect their territorial integrity.