There’s also the eCommerce category on ThemeForest if you want to build upon on something already made. http://themeforest.net/category/wordpress/ecommerce
There’s also WooCommerce, but that might overkill if you’re not selling tangible goods.
The UI may be leaving the core but it looks as the new post format functions will stay in the core. I sure hope, they are quite useful. My latest theme as well as one I’m working on now also makes use of those new functions.
+1 to the theme customizer
I haven’t put theme options in any of my recent themes, the Theme Customizer is all I use these days. I still have a theme options framework made if I ever need one.
Not getting rejected for a technicality (if submitting to ThemeForest).
Just Google it, still you should rely on plugins (or make your own plugin) for shortcodes so your buyers don’t get locked into your theme when they decide to change it.
Here’s one tutorial by Justin Tadlock (a renowned WordPress developer and theme reviewer for WP.org). http://justintadlock.com/archives/2009/05/09/using-shortcodes-to-show-members-only-content
And there’s this: http://www.wpexplorer.com/wordpress-shortcodes-page-builders/