It may be a while before the dust settles, but the next major releases of Mathics Django, Mathics Core, and mathicsscript (the CLI) will start to address
some of the long-standing graphics problems.
In Mathics Django, we now have the ability to show SVG's and 3D graphics (in three.js) not embedded in MathML mode when they are top-level objects, i.e. the graphics are are in inside lists and tables.
And we'll go from three.js circa 2013 (release 46 or so) to late last year (r124).
Tiago Cavalcante Trindade has been doing the great work to support this.
In mathicsscript we finally will have the ability to use matplotlib to show 2D images by converting SVGs to PNGs. This is done via cairosvg.
Even after this is done, there will still be a long period of cleanups and future improvements as the code is reorganized. But I am beginning to see the light at the end of what has been a very very very long tunnel.