"Unified ebook format" is a nice idea; it's not going to happen. I believe that ePub will eventually drive mobi out of the market--but PDF is here to stay. Some publications do well with reflowable formats (most novels, especially), but some really need fixed page layouts--children's books, art books, certain reference works. And PDF has a convenience far beyond its use for "books;" the ability to make consistently-printable business docs is going to keep it active.
We may see a new ebook format show up in the future, like HTML or RTF, that's easily editable to allow notes. That, too, has pros and cons; novelists won't have much use for it, but schools might, especially if edits & notes are somehow clearly marked.
The problems with DRM are different; those are likely to go away (or be diminished) as the "
sell used MP3s" ruling ripples through other media arenas. DRM makes a stronger, not weaker, case for the ability to sell or trade used digital works--after all, if someone makes an app that removes a book from your Kindle library and transfers it to someone else's, that's just like handing off a paperback, right?
I think the EULAs won't hold up to the basic logic of first-sale rights, once there's an easy way to say "I no longer have it; now this other person does." And I suspect that both Amazon and the publishers will object to that, but counterpoints may include the fact that they work very hard to convince people that they're just "buying books" in different formats, not choosing between "buy this pbook" or "license the right to access this content in ebook form." Refusing to allow first-sale rights on ebooks may require them to relabel sales sites to make it clear that an ebook is not a "sale."