As for the colours of those icons there at the moment - you could delete the theme pix-core/i folder and it would then default back to the core icons (pale grey neutral colour). Again to create a colour chooser would probably mean adjusting the output from the core JS/YUI.
That is likely to be a significant development that I probably wont get chance to do for a while, although I am conscious that I will need to spend a bit of time looking at a Moodle3.0 version, so it MAY get rolled in with that and if it is simple to do, I MAY be able to make a backport available for previous versions at that point.
More straightforward and almost certain to be added to a Mdl3.0 version, and possibly backported to other versions, would be the font-awesome icons which are not added by YUI, such as the navigation tree, the edit menu and so forth.
I will though look at adding the non-JS icons as fontawesome ones
Gradebook - Unfortunately I only have Mdl3dev on my laptop at the moment, so I'll have to take another look at 2.8 when I get chance, but I'm not seeing any issues between More and Flexibase there. Could you try changing the theme to bootstrap (Bas' theme that flexibase uses as a parent) and see what happens - I'm wondering if this is an issue that may have been fixed in the recent bootstrap theme upgrade. I'll try it out in work tomorrow where I have a 2.8 install on that PC.