I mean, yeah - /etc is messy. Every configuration file in /etc has yet another bespoke configuration language. And somewhere on your system lies a corresponding buggy, half implemented parser for it.
But /etc has gotten messy in the same way a desk gets messy. There's documents everywhere, but if you pick anything up and take a look at it, you can usually (with the help of google) figure out what that file does and how you can change it. It helps that almost every file in /etc is owned by a single program or library. And just about all of those programs have documentation. (Or, at worst, source code).
In comparison, the windows registry feels like an old, disorganized community's storage space. On first glance things look organized, but actually there's been dozens of half hearted attempts to organize everything over the years by different people, each with their own idea of where everything should go. You don't recognise half the stuff in there. Random ex-employees have been dumping random objects in there for years. But its impossible to tell at a glance what random objects are critically important, and what is trash. Everyone else has this problem too, so nobody throws anything out, and its just accreted.
Braver people than you have fallen on their swords trying to tame the windows registry. There be dragons.
I'd take /etc over the windows registry any day of the week. /etc is messy at the surface level. The windows registry is messy like a fractal.