For me it's portability. I have a LOT of documents in just straight HTML, as you say, but I can't EASILY transfer those between my PC, iPad, Kindle PW, iPhone, etc. There are all those extra files that go along with them, images, stylesheets, fonts, mp3 and video files ... (those last two were just to poke fun at the epub3 haters out there - you know who you are!)
ePub bundles all those files into a nice little zip file and allows transferring between all my devices without any issues...that's what a free and open format gives you. (Note, I don't consider the requirement to re-wrap the epub into a KF8 format for the PW an "issue" because Calibre automatically does that for me in the background...I just point the PW at my OPDS server and it gets the books I want.)
Besides, I need it in ePub format to use THE BEST reader app out there - Marvin!!
PDF is NOT an easy document format to use when reading for many reasons... but especially if the device is smaller than the page being viewed. Yes you can go through the hassle of making a new PDF with 6" pages, but if I'm going to go through that hassle, then I might as well go through the (much smaller) hassle of making it an ePub to begin with. PDF also doesn't have a lot of those "nice to have" features of a professional ereader.