In my experience, most people intuitively see _ as denoting emphasis (it’s visually lighter) and * as denoting strong importance (it’s visually heavier).
Gruber had some logical arguments behind his decision, but it ultimately seems to have been his personal preference and stubbornness that won through. Aaron Swartz, Merlin Mann and several others were advocates for _emphasis_ and *strong*, but Gruber was not convinced…
In short, you’re sort of screwed, because that’s how I write, and it’s how I’ve written since around 1992.
Unfortunately, any change to this would break backwards compatibility with legacy Markdown documents. Not to mention the habits of everyone who has used Markdown for years. Trying to get this fixed in SMD will not be easy.
That said, I think it could be done with relatively little breakage in legacy documents.
Have the spec declare that _ denotes emphasis and * denotes strong importance, while still allowing doubles (__, **) to denote the same as their respective single character. Double characters must be used to add emphasis and strong importance in the middle of words.
The breakage in legacy documents would then be:
__foo__, intended as strong importance instead come out as emphasis*bar*, intended as emphasis instead come out as strong importance
It’s mainly a semantic issue, the degrees of emphasis change. Unless I’ve overlooked something? (Not unlikely. Despite its simple syntax, Markdown is full of quirks and surprises!)
I’d love to see this getting fixed in SMD. But Markdown is in a very different position today than when Gruber made his decision back in 2006. It will not be easy to get a change like this accepted today either.