Workflow for an entity based menu system?
I have pretty much abandoned the menu system for most of my sites, or at least the main menu, in favor of Taxonomy Menu. Here is a link to my most recent site that takes advantage of Taxonomy Menu

buyagainbaby.com

The main menu there as well as all the blocks you see on the front page are done with taxonomy menu.

The types of sites I design usually categorize some type of product or other information, and it's easy to use views to do some pretty amazing things with taxonomy as arguments, which you cannot do with just the default menu terms or IDs alone.  Take a look at some of my other questions having to do with taxonomy menu, or ask any questions about implementation if you have any.