Actually I'm less troubled with these new empires, because AI will almost never create those.
There already seems to be a lot of them in people's reports.
But kingdoms of Aquitaine and those small kingdoms in HRE are created regularly.
I believe Burgundy should start as formed and held by the Emperor. He actually held the title, he just didn't use it. Lotharingia is also perfectly pukkah IMHO for anybody holding enough of its lands, which is probably the reason it didn't really exist anymore (although the HRE emperor could probably just have revived it for himself). These titles weren't really in use because the HRE Emperors didn't really feel like having them around.
On the other hand Frisia is exaggerated, Bavaria even more and Pomerania is silly. I can understand a de iure kingdom for Pomeranian pagans but come on, not one stretching the borders of the HRE far into Poland.
While I don't mind having ahistorical creatable kingdoms in areas where there was no historical kingdoms, I think that inserting fantasy kingdoms into areas which had well defined historical kingdoms is a bigger sin.
Well, I'm not sure any of those kingdoms can be unequivocally deemed to be ahistorical. Pomerania would be closest, along with Bavaria, and followed by Frisia. Burgundy, Lotharingia and even Aquitaine are IMHO historical enough, although Aquitaine is problematic.
There were no other kingdoms in France in this era and HRE had only 4 kingdoms Germany, Italy, Burgundy and Bohemia.
That true but doesn't mean there weren't some lands that could be said to have belonged in sufficiently defined other kingdoms. Definitely Lotharingia, possibly Aquitaine. I used to criticise Brittany but I was wrong and in need of reading up on the subject, which made me look stupid.
We have occasionally asked from Paradox if it's possible to have same tier vassals since CKI, but answer has always been that it's impossible to be vassal of same tier ruler. I don't know how willing they are to add grand prince and high king -tiers and if it's even possible without major overhaul of the entire game.
Well, I suppose a solution could be to add more tiers and restrict some of the tiers to specific circumstances on the technical side, while painting them as not much different from the title immediately below or above by appropriate graphics and descriptions.
Or a new type of diplomatic relationship, e.g. suzerainty of sorts, in which you couldn't do things like calling levies directly, building your own new baronies in their holding slots etc., but you could claim levies and tribute from the paramount ruler of that realm.
After all, it's not like the emperor of the HRE could have done that so directly in the kingdom of Bohemia, for example.