You're trying to fix the old, rather than improve the new.
ePub is not perfect, far from it, but it have advantage pdf will never have (openness and ease of editing). And it can still be improved.
And an other thing, when doing a mobi -> ePub conversion, it works fine. With pdf, it get a mess because pdf actually hard write headers and footer.
Right now, anything pdf is totaly unreadable on my reader. And even with reflow, still won't be. I wish some publishers with give up pdf so i can buy their e-books.
The only way pdf can think of working is having multiple version with different font size and scren size, and the publishers will never bother themselves with that.
Even Eyrolles have gotten that and they are beginning to experiment with ePub.