Using your own structure is infinitely more adaptable, and can be tailored to the specific requirements of your documentation in my experience.
However, the major downside is that keeping object changes synchronised between a customised documentation structure and the built-in metadata can be hard work - and /or require lots of clever SQL as well as manual labour that you have to run to ensure that everything is in synch.
So using the MS supplied metadata for documentation is clunky - but it tracks object evolution automatically, which is a major advantage.
So my answer is, to quote the truism - "It depends"!
However, I am only suggesting in these articles, specifically for developers who tend to avoid documentation, that there are tools and techniques that can help you do this fastidious part of a project, without too much pain.