The 80286 has the Machine Status Word (MSW), a 16 bit register. The 80386 expands this to CR0, a 32 bits register. Then 64 bit long mode adds the EFER MSR and expands CR0 to 64 bits. But even today only 11 bits of CR0 are in use and EFER has 8 active bits. I wonder why intel/AMD did not simply use the free bits of the existing register, and made that decision twice?
Probably for more robust backwards compatibility with software that might assume a given value for or write to the reserved bits. The assignment of bits to registers like this in the hardware is pretty arbitrary, there's not really any cost to using the higher bits
The flag register layout is another case of extreme backwards compatibility - its lower bits have the same definitions they had on the 8-bit 8080, even the same fixed values:
(the parity flag came all the way from the 8008 / Datapoint 2200[1], and is the inverted XOR of the result's lower 8 bits; aux carry is the carry out of bit 3, used for BCD arithmetic)
Flag bit 15 has also stayed reserved, except at one time it was used by the NEC Vxx chips for their 8080 compatibility mode. That feature had to be first unlocked by executing a special instruction, because there is code out there that loads the entire (16 bit) flag register with 0000 or FFFF. With the mode bit unlocked, that would inadvertently switch the CPU to running a completely different set of opcodes!
Particularly AMD made the 64 bit extension without any real input from Intel and didn't want to use any bits that would later conflict with a bit Intel might use in CR0. So a brand new register was in order.
The one-word answer is probably "bureaucracy". Large groups of people just don't tend to make particularly good decisions overall, and a lot of nonsensical choices arise from that.
Ditto for why CR1 and 5-7 are still "reserved" and CR8 came into existence.
https://wiki.osdev.org/CPU_Registers_x86-64#CR0.