When comparing MarkdownPad vs Zettlr, the Slant community recommends Zettlr for most people. In the question“What are the best open source Markdown editors for UNIX-like systems?” Zettlr is ranked 9th while MarkdownPad is ranked 36th. The most important reason people chose Zettlr is:
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.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Allows customizing output
A custom CSS can be added to the rendered HTML to change the preview and output.

Pro Real-time HTML Preview
MarkdownPad is split in two panes. One pane is used for writing Markdown, the other shows the rendered HTML as it's written.
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 Many features are disabled in the free version
Free version lacks features like auto-save, PDF export, Markdown tables among many others and can't be used commercially.
Con Abandoned project
Nothing from author since 03/15. Pro version preview pane crashes, no fix has been offered. See user forums.
Con Preview window crashes / does not update
Con Obtrusive, like someone WITH CAPS LOCK ON
Too loud, too much going on, and definitely an in-your-face sort of feeling.
Con Large, slow, can't open just a single .md file
