When comparing MDwiki vs Logseq, the Slant community recommends Logseq for most people. In the question“What is the best cross-platform note-taking app?” Logseq is ranked 22nd while MDwiki is ranked 70th. The most important reason people chose Logseq is:
Logseq is a privacy-first tool for thought.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Possibly more secure on web server
Due to the lack of a built-in editor MDwiki may be less susceptible to spam and defacement compared to other options when served from a web server.
Pro Doesn't require a web server
MDwiki is a self-contained JavaScript app that is very fast and can run in some web browsers such as Mozilla Firefox.
Pro Privacy-first
Logseq is a privacy-first tool for thought.
Pro Networked notes
Similar to Roam's technique of letting the notes flow with links to each other.
Pro Local-first software
Every topic is its own flat file. Nothing is better than keeping your data in the file system with an option of git source control or online backup.
https://www.inkandswitch.com/local-first/
Pro Daily journal is capture on Steriods
The daily journal feature allows you to quickly capture disparate topics under today's date and by way of tags make things organized and findable from any topic page.
Pro Open source
Logseq is opensource.
Pro Structured data over willy-nilly formatting
Lots of apps are too graphically flexible in how they allow content to be entered, placed, and formatted. They act like Word when what you want when authoring content is Markdown. Content and semantic structure, not graphical frills.
Pro Org syntax
Logseq support Emacs Org syntax out of the box.
Cons
Con External program must be used for editing
A separate program must be used to make changes to documents as MDwiki lacks a built-in editor.
Con Requires additional permissions in Google Chrome
Supposedly, you can get it to work in Google Chrome by modifying JavaScript permissions, but these same changes may decrease security.
Con Keyboard-driven editing/navigating is descent but average
It is only because I was a long-time Checkvist user that I say this. Checkvist has keyboard-driven controls which are in a league of their own.
Con Still in Alpha
Logseq is still in Alpha and is under heavy development.