As for me I believe that Apps will indeed be closed. No third party app has ever take off and yahoo had to buld themselves the photo and attachment apps which, BTW, are very nice.
I get the feeling that Microsoft's move to give up on WL Messenger to turn to Skype will also result in losing the interoperability with Y! Messenger. I get the feeling Mayer will turn to Jabber instead.
We'll probably have a much smaller header than the one implemented in neo and which resulted in several complaints
Now... should we expect the calendar coming back in to Y! Mail... not so sure ... :)