Making I/O properly programmable actually reduces complexity overall, because you can put more of the customizability on the other side if the interface, making things much simpler overall. I2C, for example, is a terrible interface in many ways, but one of the biggest is it creates a very complex and low-latency interface between the hardware and the software, and it's often easier to bitbang than use dedicated peripherals, especially the buggier ones. Running it on a small dedicated core means you can deal with it much more sensibly than trying to wrangle a hard peripheral which can't make enough assumptions about your use-case to give a good interface.