The big issue I have with HTML is that it's useless for publishing larger content, like books or even just multi-page articles. Thanks to hyper links it is of course possible to add some Next/Prev buttons to a webpage to represent such content, but those links are just hacks, not markup. eReader have developed their own formats (.ePub, .mobi, iBook, etc.) for accomplishing this task, but while they often are little more than a .zip with .html files, none of them are proper part of the Web and your regular web browser won't read them.
HTML had <link rel="next/prev"...> markup going back to HTML2.0, but it was never properly supported by any browser or developed into something that would be powerful enough to replace .ePub and Co. This to me is one of the big failures of the Web that nobody really talks about. The Web should be the place where you publish content, it should be the replacement of paper, but instead people are forced to use .ePub or .PDF for that task, as plain old HTML isn't doing the job.
The other elephant in the room are of course the hyper links. The Web still lacks any kind of content-addressability, it's all location based, thus when server go down or it's URL layout changes, all your hyperlinks break. Basic tasks like linking to a specific paragraph from another article are also not possible with HTML. Project Xanadu never got much traction, but it's really time for the Web to learn a thing or two from what they tried to accomplish back then.