Feel free to split this up into smaller issues, or do as you like - just making sure these issues are not lost:

UI en general / glitches

1. No gradebook progress var, just left-aligned percent and time
2. It seems that something strange is happening with .navbar-toggler when pretending to use a mobile window size, it seems that .navbar-toggleable-xs is expanded but nothing appears on it
3. Icons in the fake "Events key" block (calendar/view.php) look like need styling, or at least to be centered
4. I haven't found any preset where highlighted topics color and the links contained in it look good
5. May be just me, but in desktop size it seems that there could be more space between elements like headings, notifications and contents below, up to your and others consideration. I see the same in most of the pages
6. Risks icons in admin/roles/permissions.php
7. Forum posts .controlscontainer looks misaligned and would be nice if we could fix it, looks aligned in clean.
8. It seems that my chromium 52.0.2743.116 (ubuntu) (just tried firefox as well with same result) have problems rendering most of 'Readable' theme_boost/preset, they look like times new roman, is this expected? It looks weird to me (personal opinion) the mix of times new roman and the modern font used in .navbar (not sure if that is all up to the preset)
9. Would be nice to add .btn or .form-control to .search-input-form input it looks great with it and old without it surrounded by that much modernity
10. Sorry, I am not very familiar with traits. What is the benefit of having a templatable_form_element trait with export_for_template intead of having a new method in the moodlequickforms base class? $output renderer is not used, only interacts with formelements stuff and needs to be splicitly called from the form elements that needs it.
11. Actually (related with the point above) would it be too ambitious to add some boost styling to all buttons for consistency? This new theme looks really good, but cancel a backup confirm modal buttons (I guess same buttons for all confirms like 'Default competence scale) The same could be applied to select boxes.
12. When editing mode is on, there is some overlapping between course activities' completion .autocompletion icon and "Edit" drop down
13. Languages menu disappears, it appears back once you hover it
14. Filemanager buttons in "Flatly" preset are too dark. Filepicker close button is not visible. Also "Flatly", in gradebook, applies a visible #18bc9c to pair grader report cells
15. Course main page ajax dnd blocks is not working at all for me. .yui3-dd-draggable is added when I press down but I don't see much movement
16. Navigation tree's expandable nodes and link nodes are not aligned
17. inline editing help text it cutted in boost (good in clean)
18. enrol/users.php?id=xxx form buttons look modern but oversized. The "Enrol users" dialog looks like we forgot about it when adding this new theme (I'm joking about how 'nineties' it looks now comparing with the rest of the page)