The reality is that the simple protocols like SPI and I2C just are not good enough. They aren't fast, the single-ended signal scheme makes them very sensitive to noise, and there is no error correction. These protocols make sense and work extremely well for their intended purpose: connecting ICs on a PCB. If you expose an unterminated port to the outside world, all bets are off.
These protocols and variations thereof are still in heavy use in modern PCs. But they're internal busses, as the protocols intend.
I haven't looked closely at the USB spec, but I imagine the main problem with bit-banging is simply the speed required. You have to have dedicated hardware because no microcontroller is fast enough to toggle the pins while also running the software stack to decode the protocol and manage error correction.
You can run into this exact problem bit-banging I2C. With a 20MHz CPU, the maximum clock speed you can get is about 250KHz. Just a bit more than half the typical maximum rate of 400KHz. You can absolutely forget about the 1MHz version.
PHYs exist for one very good reason: it is vastly cheaper to offload comms protocols to hardware. Without that, you have to over-spec your CPU by quite a lot to get enough resources to manually manage communication. This is why every modern microcontroller contains hardware for I2C, SPI, serial, etc.
In summary, the simple serial protocols like SPI and I2C and UART are just absolutely terrible choices for external peripherals. They can't operate at reasonable speeds, they can't tolerate long cables, they can't tolerate noise. The nature and design of these protocols (excepting RS232 which is not UART) means that they cannot be used this way. There's no change to the spec you could make to support this without reinventing USB.