You can’t look at HKEY_CLASSES_ROOT and claim with a straight face it’s not complex, and it’s a central piece to how a lot of things work in Windows.

HKCR has a lot of entries, but the data underneath those entries isn't particularly complex.

Its only really big misstep (apart from the fundamental issues with the registry in general) is that file associations and COM registrations are all intermingled in the same namespace. But those can be and are interconnected (see how the Office file types handle their registrations, for example), so it's kind of understandable how they ended up where they did.

The semantics of those entries and their possible subkeys is exceedingly complex. It started out reasonably simple, but features upon features were added with each Windows release, in addition to the application-specific behaviors.

> even IIS uses .config files.

Except that is for serving from a single file share ir a replicated site across a farm of IISes.

This has nothing with 'complex configurations'