Follow the Filesystem Hierarchy Standard
Right now files are pretty much wherever, with no indication of which files and folders can be modified by the instance admin without causing problems later (when updating for example).
For example: Why are custom MRF policies in lib/pleroma/web/activity_pub/mrf/ instead of etc/pleroma/mrf/? Another example: priv/static/. It contains the default emoji (should be usr/share/pleroma/emoji/), custom emoji (var/pleroma/emoji/), default images (usr/share/images/), custom instance info (var/lib/pleroma/, since it's html and a picture), some libs and fonts (usr/lib/pleroma/), default and user set sounds (usr/pleroma/sounds/ and var/pleroma/sounds/) and the FE (usr/lib/pleroma-fe/).
It's most likely an shitload of work, but following the standard has some great advantages. It's easy to find things, it's clear to everyone which files will be overwritten by an upgrade and it'll make it far easier to package pleroma for popular GNU/Linux distributions in the future.