Part of the problem is that people don't really grok the point of Markdown. There's a reason it doesn't support tables, or a syntax for making the kind of language used in a code snippet. The point of Markdown is to mimic the conventions of ASCII-text email, both to make writing it as natural as possible, and to make Markdown pleasant to read in both ASCII and HTML.

If you want something more featureful than Markdown, the problem isn't Markdown; it's that you're using the wrong tool for the job.