I am the author of the Gnome shell extension, and I am fully aware of it having rather inconvenient icons. I tried to fit the original Syncthing icon into the Gnome style appearance. To this end, I created a new vector graphics (SVG) file in black & white colors.
If you have any idea, on how to improve the icons, please let me know. I would also be glad about any actual help anybody could offer. (Having said this, I also want to mention that I prefer unanimated icons over animated icons, as IMHO animations are just distractions.)