Why aren’t motherboards mostly USB-C by now?

While that is true, it does cause some headaches for end users. There's a (barely followed) code for differentiating the speeds of type-A connectors, but I'm not aware of any such system for type-C. Generally people expect a type-C connection to be full USB 3.2 or USB-4 speeds (not to mention the absolute state of the USB spec with them changing the nomenclature constantly). If you started putting USB 2.0 ports with type-C connectors you'd quickly find people complaining about that I'm sure.

Really, in the long term I'm sure in another CPU generation or two we'll have enough bandwidth to spare that manufacturers can start putting extra USB 3.2 or USB 4 controllers on the motherboards at which point they'll be able to replace most of the type-A ports with type-C without losing speed. In practice though I expect we'll see history repeating itself with "low" speed type-C ports and high speed type-C ports that support whatever the latest and greatest USB spec is, and no doubt some kind of distinguishing mark to differentiate them. We already see something like that with lightning, although that's just a little too proprietary to really cut it, we'll need to get something that's part of the USB spec itself.