One more suggestion for now, this time a feature request, not a bug: It would be great to be able to insert a Box, in addition to Figures and Equations.
Support for Box
They're kind of like extended asides to explain some slightly tangential point, for example http://dx.doi.org/10.1126/ science.aad8559 and http://dx.doi.org/10.1038/nrg.2015.34. And yes, numbering and cross-reference support like figures and equations would be good too.
I guess implementation=wise, they would be like mini-manuscripts within the manuscript, maybe with support for nested images and equations inside them as well, although I don't think those would usually be numbered in a Box. (Those two examples seem to be just text, but I'm pretty sure I've seen images in a Box toot)