If I'm understanding you correctly, you want users when they visit your site to have a secondary menu that has links to various points in the article. That would actually be very easy to do in Craft. It's also possible for you to paginate a page, but that would be far more in-depth.
For skip links, you would need to run over the matrix twice. You will also need an anchor matrix block. It can either be a dedicated block for anchor tags, or a header block. You run over it the first time to create your menu:
<ul class="article menu">
{% for block in entry.articleMatrix.type('header') %}
<li><a href="#{{ block.header|slugify }}">{{ block.header }}</a></li>
{% endfor %}
</ul>
Then later when you are running over your article, you can check for block type and add the id as needed:
{% if block.type == "header" %}
<h1 id="{{ block.header|slugify }}">{{ block.header }}</h1>
{% endif %}
This is a really basic example. It uses Bob Olde Hampsink's slugify plugin (it uses Craft's built in slug method). It would be better if you could determine (maybe with a drop down field in your block) what level of heading the block is. I suggest you also cache each matrix loop for performance.