First of all, it's important to distinguish that RS-232 is just a signalling convention. RS-232 requires an RS-232 transceiver, exactly the same way that USB requires a USB transceiver. Both of these technologies are for serial communication. Both of these technologies can be backed by a UART (see Catsoulis) but USB often skips the UART backend, opting for direct access instead. What you're really talking about is replacing the traditional RS-232 transceiver with a USB transceiver on devices. Sure, why not?
Reason 1) a UART is absolutely crucial for OS debugging, boot loader debugging, and recovery from corrupt nand, because it's cheap, simple, and sufficient. Often (especially when reverse engineering a device) a UART can be the only way to interact with the OS during the porting phase.
Reason 2) Although most (decent) OS have a USB stack that will work in both host and device mode simultaneously, often there is some external hardware preventing direct usage of an OTG or USB-device port (e.g. VBUS sensing). Interfacing with a UART requires no knowledge of external circuitry aside from pin configuration.
Reason 3) Lower-level 'operating systems' that run on microcontrollers or DSP often do not have such a sophisticated USB stack. UARTs are just simpler.
So now that we know complete replacement is unlikely... I can tell you that the USB console you're asking for is already here (with varying protocols). The protocol is determined by the device in question (either statically or at runtime) and will typically be one of i) CDC Ethernet / RNDIS, or ii) CDC Modem, but custom protocols are also possible.
CDC Ethernet is essentially what you're looking for in terms of 'auto-negotiating' baud rates, but you still need to configure the Ethernet / IP layers. Drivers exist for most decent host operating systems, and even Windows!
The device in question needs to have an OTG or USB-device port, neither of which you're likely to see on x86 or x86_64 chips without external hardware (AFAIK manufacturers assume that x86 chips are always the host in a USB transaction). On the other hand, most ARM SoC have had an OTG or USB-device port for years already.