I'm in favor of turning links into a custom post type and getting rid of the "wp_links" table altogether. I'm even in favor of turning links into a separate plugin from core.

I'm opposed to using the menu system for links though. You'd need to revamp the entire menus UI just to accommodate links. Plus, you'd need to add more functionality to handle features links have that menus don't (e.g., ratings, RSS, images, etc.).

Links and menus are simply not the same thing. They were built for different purposes. The author of the post doesn't seem to have a need for links. There's tons of cool things you can do with them that you can't do with nav menus. If they were turned into a separate post type, the possibilities would be endless.

The major problem is the negative connotation of "blogroll." If you look at links in that light, you're missing out on some awesome stuff.