Formations definitely need to be customizable in-game. This is a huge limitation in SE4. Formations.txt should be replaced by DefaultFormations.txt, which would function identically to the DefaultStrategyTypes.txt in SE4. It would be read form when you create your empire file, but never again. You can edit your formations in-game.
Additionally, if the script method Tesco discussed is not used, we need some way to export and import specified strategies or formations in a savegame. After a game is started, it is a pain to add a new strategy you learn of. If we could import from a list of strategies in DefaultStrategyTypes.txt, or even an arbitrary file (which is formatted correctly), so that everything in the file can just be added (or replaced/updated if a same-name strategy already exists), without having to reload _everything_ from the Default file. We should be able to export a specified set of strategies, or even all of them, to an arbitrarily defined file name. Formations should work in just the same way. Both of these functions would be useable during any turn of a game in progress, and imports would add the formations and strategies to those saved for your empire (which would naturally need to be exported with the empire file when you export that).
An additional benefit of the above method is that we would be able to edit formations and strategies to be saved for a mod or custom file to post in a graphical interface instead of a text editor. They should still be saved in text files so that those that want to use a text editor can do so, of course. But, editing and creating formations in a text editor is a huge PITA.
Speaking of empire files... when we edit a saved empire file before starting a game, we should have an option to either keep the strategies and formations saved in it, or to load them from the default files (a separate toggle for each). Default would be to keep what is saved in the empire file. Another toggle should be present to either keep all ship designs saved with the empire file, or to clear them. Many players like to save their empire file and use it in a new PBW game, maybe with a few tweaks here and there. The problem is that if the empire file is edited in any way, saved strategies and vehicle designs are lost.
Personally, I don't mind if empire files start ranging in the dozens (or even a few hundreds) of kilobytes instead of 10 or 20 if there is a lot of data saved in them (many user-defined strategies and formations to get to 100s of KBs), and I doubt many people would. It would IMO be an acceptable tradeoff for the added functionality.