I don't like how much information we're losing. On the old system, we saw all the information that was relevant: have we read it, what's the title, who's it with, how recently have either person sent a message, and how many messages are there anyway. We also had the ability to select multiple messages and perform actions on them, like archive them and delete them (actually, those were the two).
Now, we see who it's with, sometimes the title, how recent the last received message was (not how recent the last sent one was, which is useful information), and how many messages are in the conversation (though it's not necessarily intuitive that that's what that number represents). We can't see whether it's a new message, we can't delete conversations, we can't archive anything, we can't act on multiple conversations at once... For the sake of a new layout, we lost all but the most basic functionality, a lot of meta-information, and IMO it's a less user friendly layout as well. The one good thing about it is that we have in-page replies, but couldn't that have just been added to the previous version?
Summary: I don't like it. Rather than improving what was already there, this feels like a worse replacement. I'd have much rather seen the current layout made to look better, and missing functionality added (like multi-user messaging, or the in-page replies). At least, that's my opinion.
Although a fanboy for the RT page for a couple of years, I recently made up my mind and created my own profile. So far so good I like the page, it's easy to use :), but then again never used the old one.
Rather than having the message lists relocated to the side with the most recent message auto-open in the main body of the screen, can we have the list remain in the main body, and use the sidebar to group multiple messages with the same person into "Conversations with [username]"?
That way if you're trying to find something you and a specific person talked about once, you can go just into messages with *that person* and scroll through the various topics instead of trying to wade through what might be months of message topics with other people.
The main body would be a list of all conversations individually, and the side would be grouped per conversation partner.
Also, as said above, mass-messaging (though I agree it would open up the possibility of spam), so perhaps only able to do this with those on your friends list. (Then if you tend to spam, you'll likely tend to lose friends, and the problem will resolve itself.) The ability to delete multiple messages at once, multiple conversations at once, or whole groups of conversations at once; the ability to sort by either received or sent in ascending or descending order, and adequate notification of new messages.
Also, for the message alert on the page header by your avatar, instead of just saying "you have new alerts" can message alerts have the "Message" link put in red with the number of new messages, so something like:  New Messages. That way if you have new message alerts, you can go directly to the message screen instead of having to first go to your profile to see that it was a new message.
Group messages would be great, too. (or... wait, do we already have that? i.e. send a message to everyone in a particular group?)