The major improvement for me is the ability to use faceted classification systems. If I need a classification system at all, that is. In most cases it is an utter waste of time that just soothes some kind of OCD-leaning anxiety.
Mind you: having worked as an Information Architect for some years I can totally relate to the notion of constructing arcane taxonomies for one’s notes. 
Alas in the end I found that as a consequence of that you always spend way too much time on filing information (the more notes you have the worse it gets) and far not enough time on productive thinking/writing.
Hence I’ve started to throw out most classifications in favour of strong connections (i. e. direct contextual links).
Here is what I currently still keep using:
- key type categories: projects (actionable, finite with an outcome), areas (actionable, infinite), resources/references (not actionable), indices and MOCs (the more meaningful main substitute for file system folders).
- subject categories (e. g. people, organisations, locations, media, cadences), all of them with some flat hierarchies, e.g. people/friends, people/family, people/authors, people/network, media/books, media/articles, loc/Berlin, daily/morning, …) – loosely informed by LATCH (⇒ UnLATCHed: Richard Saul Wurman’s Theory of Limitations | Isis Information Services)
- process states (mainly for projects, i. e. projects/options, projects/later, projects/next, projects/WIP, projects/evaluate, projects/completed)
- GTD contexts (with a bit of hierarchy, e. g.
@private/home/kitchen,@work/meetings/1on1, …) - action and content tags (e. g.
#decision,#idea,#observation,#insight,#belief,#assumption,#write,#follow-up,#expand,#prune,#clarify, …)
All namespaces as flat/simple as possible and never deeper than 4 levels. Most tags within a hierarchy are aliased to their last component in order to keep my notes free from clutter and speed up writing ( e. g. @private/home/kitchen => @kitchen).
Basically the vast majority of classifications in my graph exists to help me organise/structure work (actions) rather than information (notes/writing/thinking). For the latter direct links are way more useful and productive. Takes a while to let go of some habits acquired via managing more structured data (literature references, whatever…) but it’s totally worth it. For me that is. YMMV. 