In Linux, no doubt there's alot to get your head around, but I've never found things to be a giant pile of spaghetti. The challenge Linux has is there's a bajillion ways to do things so you have to be pretty experienced to feel confident crawling around the tunnels and ventilation ducts.
To be honest (and I'm aware that I might be tarred and feathered for this) I kinda prefer the centralized Windows registry to the "random assortment of config files" approach that Linux has. I think both Windows and Linux give you that feeling of carefully crawling around in ventilation ducts once you get your hands dirty; I doubt it's possible to get rid of that without getting rid of the inherent flexibility that the systems provide. There's a reason Windows has both the registry and the Settings app.