I wish there was some kind of desktop application that I could sit down and locally organize my data into, allowing me to keep a full quality source while syncing a copy to naturalist for others to benefit from.
As it stands, I don’t really have a system in place, and I don’t want to put a lot of effort into a lossy (assets get compressed and stripped of metadata) online project.
iNaturalist would agree with you; they explicitly say[1] it's not meant to be the primary source for your photos. Users generally fall into a couple broad camps:
1. Mostly use the mobile app, and take photos and upload observations directly from there. Local photo collection either isn't a priority or is backed up by their phone's cloud sync.
2. Mostly use inaturalist.org via a desktop browser, with either a standalone digital camera or mobile photos synced to desktop. Local filesystem (hopefully plus backups) is the source of truth.
I have been working on a desktop application[2] with a long-term goal of full bidirectional sync, and a secondary goal of offline usage. The current feature set is fairly modest and read-only, though, focusing on organizing local photos using data from iNat.
[1] https://www.inaturalist.org/pages/about
[2] https://github.com/pyinat/naturtag