Portability. If you have to send a presentation around, embedding fonts in PowerPoint only works if the viewer is on a Windows machine, and keynote is not an option if your viewer is on a PC.
One is that you can't have speaker notes integrated in the presentation the same way you can with PP or reveal.js.
The other one is that it doesn't scale. You export the slides in one display ratio and it stays like that. Most web presentation formats will adjust to whatever your display is doing.
I often have complex animations and embedded video that will not survive the PDF export, and am sending presentations to people who can't just be asked to install libreoffice.