I'm happy with all changes and new features you develop for the new blog - Tag cloud, Category menu and Archive widget were much needed to come back! Yet, some of them is "half baked" to my opinion, and especially all menu issues. 
The current category menu enables to hide the "all" category - very useful, indeed! But then we can not toggle other categories, so It's not a real "custom menu", but only "a menu without the 'all' category". Beside that - the vertical design is a good option to add, but what if I need a horizontal design? apparently, I can switch off the "all" only in a vertical design. I'd like to suggest a different attitude to the whole problem.
OK, maybe somewhere we need to find (hidden or not) the basic 'all posts' feed, for technical reasons, but instead of custom feeds and custom menus - why not combining them all in one place? we will have one "feed" widget to use, and within it we could choose A. Weather to show or hide the menu altogether B. Toggle the categories in the menu ( and what is checked in this list, will also appear for the viewers.) In that case we could have an "all posts feed", "one category feed", or "some categories feed", all in one place. Whatever you check will be displayed, weather you choose to show or to hide the menu altogether (or replace it with a separate menu). Of course it will be even better to show or hide categories in the displayed menu. And to add other hidden tags except for "featured"- tags we can use for filtering the feeds. 
An example : A page that shows cakes ,cookies and deserts recipes, all vegan, all from red ingredients. The menu will show "cakes | cookies | deserts" but I would like the "red" (which is only for me) to be a hidden tag , and the "vegan" to be a hidden category. Thanks
