Markdown or WYSIWYG?

I would go with something simple that just targets a textarea, since markdown is just plain text after all, and really an editor is not at all necessary for markdown, but if you really want one, just targeting an existing textarea on the page is a simple solution.

In fact, I'd say start with just the textarea, and add the js editor on top of it later if you feel you really need it, I suspect you won't really need it. Just learn markdown syntax, it doesn't take too long to pick up, and once you do, the editor is superfluous. :)

I am currently building a personal blog and I'll use markdown because it seems like it's easier from a usability point of view. I already prefer markdown over any of those full featured editors with buttons.

I would go with Markdown. It's easy to read and write, especially if you touch-type.

You asked which would give you a better result. For most things, the result will be exactly the same. However, there are some details to consider regardless of which system you choose:

• How will you deal with typographic niceties such as proper apostrophes, dashes, and quote marks? These characters do not exist on your keyboard. Do they matter to you?
• Do you need to add images? How will you do that?

Both Markdown and WYSIWYG editors can potentially handle these issues. But for example, you might need some way to upload an image to your server.

Overall, I reckon using Markdown has the potential for higher quality results, because you can add additional parsing steps yourself. For example, your parser could automatically convert all single prime marks (') into apostrophes (’). And while a WYSIWYG editor could potentially do this for you, it would be difficult to add the feature if it's not already there; and if the feature is there, can you override it when desired?

I would recommend using a CommonMark-compliant parser. I use this one. Once you have that working, you might wish to add your own parser, which could run either before or after the markdown conversion.

(For the record: I'm using Markdown for my content, but I haven't gotten around to adding my own parser yet.)