I think this or something to this effect would be great for improving the menus. I too have found the same issues you have mentioned, and on one site I currently have 4 custom post types and 4 taxonomies, with plans for more of both too. So you can imagine how long the page gets if I were to open them all up.

I've also found that if you have a reeeally long list of child menu items, say you add a whole list of all the terms of a tax for instance, they are all randomly added, in no particular list. And when the list is longer than the page, you have to scroll to find them, and if you want to put one of the last ones at the top of the menu, well scrolling while dragging is not only slooow but also very hard and annoying with a mousepad.

There are definite needs for looking more into making the system better in many ways. This is a good start you have. :)