Windows up to 3.0 had a fairly reasonable (though still quite imperfect, a remnant from DOS) flat file configuration, similar to Unix and Unix-like systems. You had your BOOT.INI, SYSTEM.INI, WIN.INI and it was relatively straightforward.
The introduction of the registry in 3.1 definitely made things more complicated, but it was still under control to a degree. Afterwards, however, Microsoft blew it completely. The registry has now become some arcane, cryptic and volatile pseudo-filesystem that is hard to navigate, clogs up faster than a Hummer burns fuel and leaves tons of remnants, while slowing performance and being a point of risk.
Registry syntax is also unintuitive and doesn't seem as if it follows any consistency whatsoever. There are some tools that make using it a little less painful, but it's still superfluous. You have both registry keys and plaintext configuration files scattered across your system, in all sorts of locations.
Unix got it short and simple. The registry has been a total clusterfuck for a long time now and you are by no means the only one. Plenty of people before you have expressed the same sentiments and in far greater detail. It's no secret that the registry sucks.