The Fairphone 3 is 9.9mm thick vs 15mm in the Librem 5. The Snapdragon 632 (14nm) in the Fairphone 3 is more energy efficient and its CPU (4x 1.8GHz Cortex-A73 & 4x <=1.8GHz Cortex-A53) is roughly 3 times more powerful than the i.MX 8M Quad and its GPU is roughly twice as powerful. Because the Librem 5 will have to do most of its video decoding and encoding in software, the Fairphone will be cool when watching video, whereas the Librem 5 will run hot and drain the battery.
The resolution of the cameras in the Fairphone 3 is basically the same as the Librem 5, but the Fairphone will probably be much faster, because it has a digital signal processor and image signal processor in the 632, plus it has a dual pixel PDAF, so its auto-focus will probably be better (although we don’t know at this point, what camera hardware the Librem 5 will have.
The Fairphone 2 was able to be opened without tools, but it looks like the Fairphone 3 will require a screwdriver, so it isn’t as unique in its modular design, but it is also 1mm thinner than the previous version. The new translucent case is a nice touch. The Librem 5 will probably be a little more difficult to repair if you want to do something like change the screen or replace the battery, but the Librem 5 is the only phone in the world that allows you to replace the cellular modem and Wi-Fi/Bluetooth. Plus, the Librem 5 is likely to get over a decade of software updates because it is based on Linux, whereas the Fairphone 3 will have more trouble providing software upgrades, due to Google’s compatibility tests.
If you want a phone that just works, get the Fairphone 3. If you want the most interesting phone that has been released in a decade, get the Librem 5. I mean that literally. See my list of innovations in mobile phones. Despite the fact that its hardware is outdated, the Librem 5 will be one of the most innovative phones ever created.