I am in the process of rewriting my Elemental theme framework and, apart from the breadcrumbs (I loves my breadcrumbs system) it does everything you are suggesting above.

What I am doing with it is adding support for popular plugins that add support for major features. Currently it has support for bbpress and I am working on support for jigoshop. When I say support - obviously bbpress would work anyway, but I am making sure the styles fit the design of the theme nicely and work in all child themes. I am also making sure there aren't two sets of breadcrumbs running (since jigoshop also includes it's own breadcrumbs system), and a few other niceties.

One thing I hadn't put much thought into is WordPress post types so I am going to make a note to make sure they look good as well. Maybe I could support the WooTumblog plugin or something similar.

So far I have removed about 20% of the code from Elemental version 1 - and I plan to keep going. I have also added native support for more built in WordPress features. In terms of customising the layout (different sidebars etc) I have some ideas of how I can do this without bloating the theme with loads of code. Hopefully they will work :)

I am going to follow this thread with interest as there's a lot of good feedback in the comments and I hope to use as much of it as I can to make Elemental 2 as flexible as possible without treading on the toes of WordPress built in systems and concepts.