I use pdf files, generated with Beamer/LaTeX, and whatever pdf viewer is available on the computer I am presenting on. While I like the Beamer/LaTeX/PDF combination better than PowerPoint type applications I am not particularly happy with its ability to embed media (sounds and videos). Further, common PDF viewers (e.g., Acrobat, Evince, and Okular) do not provide any type of "presenter" view with a clock and notes on one screen and the slides on a projector. The presenter view in advanced viewers like impressive are pretty limited. I am thinking of switching to an HTML5 based system (possibly reveal.js), but wanted to know what the drawbacks of HTML5 based presentations are.
Overall HTML5 Presentations are great, but that's not to say that they'll be better than the alternatives in every respect, or that you'll never have a bad time.
One challenge I've experienced is when I need to collaborate with colleagues on the presentation -- many lay people are intimidated by HTML or Markdown-based tools. There aren't a lot of cloud collaboration apps that will let you upload plain HTML/Markdown and then let your friends add, edit, or comment on your work. You may end up having to do a lot of converting back and forth between HTML and Office formats if you work with non-techie collaborators.
Similarly, people are often confused about how to open an HTML presentation when you send them an index.html file and a folder full of assets. You can remedy this by hosting things yourself in a Dropbox folder, but that isn't always awesome.
I use Reveal.js often, but I think it's fair to say that I spend more time developing an HTML presentation than I would in Apple Keynote. I usually write out my ideas in Markdown first, then convert that to HTML and edit it further within the Reveal.js codeset (from my code editor).
If your presentations are mostly made up of text and un-altered images, Markdown/HTML can be very fast. If you like to futz with the colors, fonts, and modify your images, that's faster in a presentation software like Keynote. Even simple things like cropping images, writing over images, etc. would require you to do them in an external graphics editor before incorporating them into your HTML presentation.
So basically the biggest problems with HTML presentations are working with other people and focusing too much on the visuals. Other than that, it's great.