I give a lot of talks, and would move to HTML5 presentations in a second -- but the editing tools just aren't there yet. Sometimes I really just want to draw some shapes and show the relationships between them without having to go to a separate editor for that.
The best tool out there right now is http://slid.es but it doesn't come close to letting you represent things visually.
There are tools that let you draw on the screen, no matter what other applications are running. At least there are such tools for Linux, but I'd guess there also would be one for Windows. Heck, I'd guess there is such a tool as a browser bockmarklet. If not, tell me and I write you one (would support Chrome and Firefox and maybe, just maybe, IE11 (canvas+pointer-events:none)).
Right about the editing tools. I'm hoping that security exploits such as this will cause governments and big corporations to start demanding safer document formats (especially for public or other widespread data interchange), which will drive the market for better editing tools. I certainly agree that ease of creation is a major limiting factor right now.
This reminds me that MS used to have an export to HTML feature in PowerPoint, but it was very IE specific and they removed it in PowerPoint 2010 I think instead of fixing it. This is also true for Word/Excel, to the point that even in the 2013 release you can set it so that it generates HTML that even MS's own IE10 won't render properly.
The best tool out there right now is http://slid.es but it doesn't come close to letting you represent things visually.