When comparing vimwiki plugin for vim vs Zettlr, the Slant community recommends vimwiki plugin for vim for most people. In the question“What is the best cross-platform note-taking app?” vimwiki plugin for vim is ranked 23rd while Zettlr is ranked 49th.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Internal link makes it easy to create a knowledge network
Pro Comfortable for Vim users
Has a very minimal learning curve for people already used to Vim, as the preset shortcuts are very easy to learn and don't conflict badly with other Vim behaviors.
Pro Focuses on writers
While many Markdown editors don't offer specific support for a certain type of workflow, or offer features for scientific workflows only, Zettlr offers features that help the writing process of journalists or researchers in the arts and humanities. It's a lot more text-focused than most editors.
Pro Citation support
While it supports a diverse range of syntax (chart, easy image insert, etc.) found in other editors, the great citation support made it possible to write real articles. Citation from Zotero and Mendeley can be inserted easily which is a huge plus.
Pro Almost perfect
This is the best option, still not perfect, there are some bugs like creating / editing tables and resizing images, but the PROS destroy the CONS, easy quotes, WYSIWYM , attachments tab (supports attaching and opening links to any file), table of contents, TAGs, easy hyperlink between files (same as citations), export to many formats (like Word, HTML5, PDF)...
Pro Renders math in-place through KaTex
Cons
Con Limited to use with vim only
vimwiki is a plugin for vim, so you won't be able to make use of it if you're not a vim user (and don't want to be).
Con Obtrusive, like someone WITH CAPS LOCK ON
Too loud, too much going on, and definitely an in-your-face sort of feeling.