I'm trying Version 3.6-beta2 on a MultiSite installation.
Lovely piece of coding! But a thing I noticed is that Custom Page Types doesn't list in the accordion to the left when I create and edit menues in admin.
It only lists Pages, Links, and Categories (and theme twenty thirteen shows the Format option as well.
On 3.5 I can see all my CPT listed here under Pages as well, making it very easy to add any content to my menues.
Bug or "feature"?