In HTML superscript and subscript tags may simply be nested:
10<sup>10<sup>10</sup></sup>
Markdown implementations ... vary, but typically either a ^<text><whitespace> or ^<text>^ block indicates superscript. That .. doesn't permit nesting: 10^10^10
or: 10^10^10^^
... either way is ... ambiguous or undefined. HTML's start/end tag syntax wins.More generally, where simply writing text, the notion of having bounded blocks and pairs can become confusing, especially where <div>, <section>, or <article> tags are used. I'll frequently find myself unbalanced in those. To the extent that Markdown allows me to Just F*cking Write and not worry about markup ... that's a win. Ironically, for all its reputation for fiddlyness, LaTeX's use of a double carriage return as a paragraph delimiter affords a similar simplicity to much straight prose.
Markdown extension of course vary, but my point remains that using Pandoc (my usual approach), I have as first-class ready-at-hand elements tables of contents and footnotes, both of which I use extensively. I don't have a good formula-entry capability, for which I'd turn instead to LaTeX. I'd also argue that basic table entry in Markdown beats HTML, and is moreover very easy to script given structured input, e.g., with a sed or awk one-liner.
The fact that you seem to be focusing on short content rather than longer pieces may explain some of our differences of views. My typical focus is essay-to-book-length text-heavy documents. If I'm kicking out a short HTML fragment, sure, just code it up directly. Where I'm writing a work which is not specifically intended for the Web, but which could include HTML among other formats, Markdown and LaTeX start making far more sense.
I find complaining about hypertext references to streamline discussion and avoid duplicate content a ... curious gripe in the context of hypertext-authoring tools, but power to you.