How many times do people flip cultures? Seriously, I might flip once in an entire play through, if at all. For me this is just the cost of doing business on the rare occasions that I do actually change. I often make it a point to actively maintaining my Initial culture all game, especially if it's rare or a minority one.
I agree that it makes more sense to tie it to the local culture, no the ruler though.
I've had it happen 4 times in the first few hundred years. I can game it so it doesn't happen but here's the scenario where I ran into it:
1: had sons
2: gave sons land in northern italy, because I had it to spare
3: sons accepted local culture. (somehow they went from frisian to lombard) (also possible: accidentally pick wrong tutor)
4: sons had kids
5: ruler dies after his grandchildren reach adulthood. switch to his son who is lombard and has lombard children
6: switch new rules to frisian culture, as these are the majority of my land (later this becomes dutch)
7: rulers children (matured) are still lombard. their children are lombard.
I can avoid this by:
1: not give children land at the cost of prestige. This takes away from the RP aspect
2: demand my grandchildren get educated by me or another frisian noble, which can be a pain if I need to do it for every child. By the time I noticed it I took inventory and my 3 sons had between 1 and 4 sons of their own. that's 7 times waiting till the grandchild is 6
3: assassinate all other grandchildren and bank on no plague killing off my peeps.
If you never choose an odd educator or give your children land outside of your primary culture then this might not be an issue, but I ran into it quite a bit. I think in my game i'm now safe again, I've inherited (as a lombard) early enough so that the (4th generation grandson) before I had kids. now I've switched to dutch (new culture of my lands) and children should be dutch too
And none of those kids will get any land anytime soon I can tell you