There is a lot of room between the bare metal and stdio. You have said you aren't writing an OS kernel, but not whether or not you are running under an OS.
Running directly on hardware without an OS, you will still want to encapsulate all of your I/O operations in a module, even if you don't formally define a device driver interface and framework for all of your I/O modules to follow. This is hugely architecture dependent, and makes you responsible for knowing all of the details of interaction with every I/O device you might ever use. For some devices, this can quickly become a huge development effort. That isn't a problem for embedded systems, but running on commercial hardware this way is neither easy nor recommended.
Running within an OS, you probably don't get (and shouldn't want to get) access to the actual hardware registers and interrupts. If you are developing a custom I/O device, the best practice is to make it conform to existing standards so that you need as little low level custom software for it as possible. This is why you see a lot of custom user interface gadgets connecting via USB and identifying themselves as HIDs (Human Interface Devices). As a HID, the existing USB drivers take care of the physical layer, and the OS-supplied HID driver takes care of the logical interface, providing a very simple high level access API to the application.
One of the operating system's key roles is to provide a consistent I/O API across all devices. Generally, that takes the form of open(), close(), read(), write(), and ioctl() functions (the names vary, but some form of at least the first four will always exist). The OS layer is quite raw, however. Typically, an OS call is forwarded without much processing to a device driver, which then forwards the data on to the device. Usually, the OS low level calls block the caller until they complete, and often they have restrictions on the sizes of the buffers that make sense. For instance, raw access to a disk device is usually required to be for an integral number of disk blocks at a time.
And don't forget about things like file systems and network protocols... all of which are made much more reliable and compatible by encapsulation within an operating system.
Even if it is acceptable to call read() and write() for single characters, that is usually not the best performance possible. Operating system calls are relatively expensive, and if you can read multiple characters in a single call, your performance can go way up.
That is the origin of the stdio library for C, and various other buffering libraries in other environments. The stdio library provides a buffering layer that isolates the C code from the block size of the underlying hardware. Even on an entirely home-grown operating system where you have full control over all the devices, something like C stdio will still be valuable.
Writing your own stdio replacement is a highly valuable exercise, even if you don't use it in production code, and is one I would recommend to anyone wanting to learn about what really goes on between printf() and scanf() and the terminal or files.
One valuable resource is the book The Standard C Library by P.J. Plauger. In it, the author presents an implementation of the complete C runtime library specified in the ANSI standard. His discussion of the specific implementation choices he made is valuable and apropos to the context of this question, and the discussions of why some of the standard library features were specified is interesting as well.