There’s definitely a lot of shortcode plugins out there, but I think it would be useful (to me at least) to have better columns that use the GP grid, and some matching buttons, toggles etc..
Menus would definitely be a good one.
I’m almost done building the Featured Widgets add-on, which adds the same amount of widgets as the footer below the header. As for placing widgets inside posts/pages, this plugin is great: https://wordpress.org/plugins/widget-shortcode/
Definitely something to look into, although I think Disqus is the best comment system and should be used in most cases.
Shortcodes should already be allowed in widgets by default.