Dotted Boxes:
I think this is fixed in the latest version on github (the dotted boxes only appear when a block is actually being dragged, not just when editing is turned on) and just waiting a few issues and some feedback from HQ over code_checker testing before releasing a minor update to the plugins database. The code all works and is stable but the code_checker is reporting line indent style issues that are incorrect and can't just be 'reflowed' based on the code_checker reporting - Eloy at HQ is investigating.
Bootstrap2 v Bootstrap3:
Some of the code you use can be added with the relevant classes from both without clashing (e.g. you can use the grids or the button classes from both). But obviously some exists only in the one and need some kind of fall back (e.g. panels do not exist in BS2).
One way of providing that fall-back is to copy and paste the css for panels (as an example) into the BS2 theme customcss. That will work in most cases that do not rely on any of the BS javascript - of course being bootstrap and responsive flexibase itself should work on mobiles anyway
Location of CustomCSS:
I did consider putting CustomCSS and CustomLESS on their own 'custom' page, but haven't done so to date, I'm not sure if that's a good idea or not, but happy to take User feedback on it. I don't really like to put it at the top of a page with other settings - its kind of psychological thing that customcss overrides everything else so comes after it, and yet I realise that it doesn't really matter where it appears on the page, that's simply down to where it is in the code, and I also realise that by the same logic, it shouldn't really be on the first page either So if anyone has a good UX reason for moving it to a different page, such as with the customLESS, then I'm open to such suggestions for the future.
Fonts:
I obviously need to clarify the instructions/comments with the setting, or work on developing the setting - It is currently only designed to take one font name (such as the web-fonts above) e.g. "Times New Roman", with the font type e.g. "Serif" in the other setting, but not a series of fall backs like Tahoma, Geneva, sans-serif.
This Course:
I'm glad you (and your users) like the feature Derek, I do to. I'd like to give credit where its due, but I can't remember which theme I saw this in first - it's in a few now, so obviously quite a lot of people agree with you. I think in this instance I 'borrowed' the code from bcu, but it could just as easily have been from essential as I know both have the feature and I have used code from both in various parts of flexibase (and credited both, and others, for the ideas and hard work put in by all the developers! ).
Hopefully flexibase is a mix of some of the most popular features of the best themes out there (like this) as well as some new things (like the flexbox layout, the layout options, the LESS settings and now the Theme help pages and navigation between settings pages) and hopefully others will 'borrow' some of those features for their own themes too so that we can all improve the user experience for everyone