I can drag to create internal references, and drag stuff between projects without losing order, structure, keywords, notes, or external references. Yay!
The new hover interface, on the other hand, is kind of "meh". I find it actually harder now to make something a child of something else, because I have to wait for the state to change. Before, I could just hover and go. (I can see where the new approach might be helpful for people who do a lot of in-binder linear reorganization, but I personally do most of that by shuffling corkboard cards.) It also doesn't fix a peeve I had with the old d&d, which was that collapsed folders and documents don't open when you hover on them.
It's ALSO harder to put things between other things (although, as I said, I don't do it that often vs. using the corkboard). The reason is that when I try to position something and stop to check if I have it in the right spot, that's just the moment when the throbber appears and distracts me. While I'm frozen in brief confusion, trying to figure out which of the lines means what, it switches to child-drop mode and I'm now stuck. It feels like I'm playing some weird sort of video game, and mostly losing.

I would rather see something closer to the old d&d mode put back, with one change: when you hover a d&d over a collapsed folder or document, expand it after a short delay, the way firefox bookmarks, Windows explorer, and other such programs do it.
I realize this doesn't address the situation of a folder or document that doesn't have any children, but you want to add something to it... so in that case, after the hovering interval, instead of throbbing the icon, why not throb the [+] (expand/contract) box in front of the item? This would then be an indicator that the folder or document is now "expanded" and you can drop something in it. (Once this happened, dropping would make a child, just like now.)
Functionally, this would be just the same as the new d&d (i.e., hover a moment to drop a child instead of a sibling), but without the visual noise and with the added benefit of making it easier to move things inside collapsed documents or folders.
Make sense?
(Oh, almost forgot: it'd also be nice if you could d&d between collections and the binder - I would LOVE to be able to have a "templates" collection and then ctrl-drag new documents from there into the binder. If "expand on hover" worked for the collection/binder tabs as well as individual documents or folders, I'd be able to do that.)