Fish 3.4 was released a few weeks ago and allows users to set fish_color_* variables from *.theme files with fish_config theme choose/save <theme name>. (changelog)

Custom themes can be used by placing them in ~/.config/fish/themes/ and it would be really convenient if Fisher could place themes from plugins here.

I think the best way to do this would be to just have the same logic used for functions. So plugin/themes/*.theme could get installed to ~/.config/fish/themes/ the same way plugin/functions/*.fish get installed to ~/.config/fish/functions/ by Fisher.