I use Rmarkdown with slidy mostly. I like it because I can use html tags outside of r code chunks (perhaps it is do-able in other formats, no idea). However I run into trouble with indented lists.
---
title: "Test"
author: "Me"
date: "Today"
output:
slidy_presentation
---
## Test Slide
<ul>
<li>One Bullet Point
</ul>
This works like a charm.
Output (html):
<div id="test-slide" class="slide section level2">
<h1>Test Slide</h1>
<ul>
<li>
One Bullet Point
</ul>
</div>
However:
## Test Slide Indented
<ul>
<li>One Bullet Point
<ul>
<li>One Indented Bullet Point
</ul>
</ul>
Causes trouble. Output (html again):
<div id="test-slide-indented" class="slide section level2">
<h1>Test Slide</h1>
<ul>
<li>
One Bullet Point
<ul>
<pre><code> <li>One Indented Bullet Point</code></pre>
</ul>
</ul>
</div>
And thus "list within the list" appears as a code chunk rather than an indented list in the html document.
You have four spaces preceding the line with the list element. This means that pandoc will interpret that line as a code chunk. As far as I know there's no option to prevent this, so you will need to remove the indenting before the html tags.
http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#verbatim-code-blocks
I will also point out that markdown supports nested lists so there's no need to use html tags in your example:
- One bullet point
+ One indented bullet