I am reminded of (but unable to find...) the Joel on Software essay that noted that it's always trivial to write simple, unbloated software, until people realise that they all have a different, lightly overlapping 10% of features that they need.
Most people use the same basic features -- let's say they use 18% of same stuff, and 2% of more unique to them features.
The rise of "lightweight" apps that tons of people use has proven that taking out the bloat is possible for most people (e.g. casual users can work with Pixelmator or Acorn just fine, don't need Photoshop).
Vertical market software tends to have very specific requirements which are unfortunately not agreed upon by all of the big players in the industry. So you can simplify it, but if your software doesn't support X, Y and Z then you can't sign Corporation Foo. And you start getting feature requests (er, orders some might say) from your bigger clients who are paying for thousands of subscriptions/licenses. But Corporation Bar doesn't like that - so it has to go in as an option/preference. Repeat this process for about 5 years and you have what appears to be a bloated piece of software.
Proper Markdown and footnote support is usually one of those things.
Nonetheless it's an interesting question - hundreds??
Is there a reason, why someone can't use a similar theme and markdown plugin with wordpress to achieve the same?