Yeah you're absolutely right. RST was great when Markdown wasn't around, but Markdown is just better.
It's a bit of a toughie, the python community doesn't have much to deal with Markdown itself. pypi expects rst etc. There's also very few tools available in general, which is a huge shame.
Part of this is due to different Markdown "flavours". At this point though, Github being the largest provider of Markdown, a safe bet would be to standardize on Github's flavour and call it a day.