1) Nested comments. No need to nest them. The same effect can be achieved by indenting each comment in the style sheet e.g. depth-2 [margin-left:30px} depth-3 {margin-left:50px}
Nesting the comments makes it painful to style them, as can be seen by trawling the internet - no one really bothers.
2)Custom post types. As far as I can see they only work properly if edit_posts capability is also added to the role i.e every role accessing a custom post type will then find that the custom post type also has an Add New Post icon. Would be glad to be proved wrong. Currently I get error messages (not allowed to edit this post) every time auto-save kicks in, and all taxonomies are disabled unless a role is given edit_posts capabilities.
3)Custom post types. Access to the Admin screen for a role requires read capability i.e. the Dashboard icon is visible. Not neat, though I understand a snippet of code will remove it.