Alex, is there any chance that mod updates in the future would stop breaking saves? Some change you can do on your end? I believe that is the main barrier to any sort of mod manager that a lot of other games have.
The problem is that mod updates may just be balance passes, tweaking damage or ship values here and there, and those can be eaten rather easily by the engine because it doesn't change anything outside the battle screen, really.
The problem usually hits when mod authors add new ships and/or change fleet lists, or more often when something is deleted, or faction/colony behaviors. If there's a fleet generated in the universe (in your save file) with ship X, and ship X is removed... The game doesn't know what to do, because it's looking for assets that don't exist.
As well, the economy and marketplace is paying attention to factional information, like what fleet behaviors are expected. Let's say you have some, like, mod that adds a "religious" faction that has "crusade" fleets that do x, y, and z behaviors. If the mod author releases an update removing the "crusade" as a fleet, or redefining properties of it, the engine doesn't know how to use that fleet anymore, and if its actions are based on "crusade_fleet" behaviors, and it's referring to that file, except "crusade_fleet" doesn't exist... Exception.
There's really no non-breaking way I can think of to deal with this fault because, well, they're specific to mods. As Alex only changes fleet compositions and behaviors, and adds or subtracts stuff, during updates, and (especially since, as we all know, this is still a game in development and player progress loss is to be expected) he tells us "start a new game" (or recommends it at least), I don't fault him for not trying to add some sort of placeholder effect or replacement for such cases.
Edit: don't take this the wrong way, but i feel like you're putting undue trust in the game's developer for support of modding idiosyncrasies, when virtually every game ever with a modding scene (note, I am not talking about "editors" like say, Halo Forge, as they are built into the engine as a feature the everyday user can access) has the implicit lack of support for user generated content.
You could argue Bethesda, with its Creation Club, shows that it is possible for devs to directly offer support for mods, but they offer only limited support even in these cases, and only specifically for the bare handful of mods they've curated (and basically turned into bite-sized DLC), AND all of which don't do anything fancy requiring third party code (Skyrim Script Extender in this case). Anything you get "in the wild" is as-is and the devs have precisely zero responsibility to account for all UGC.
Now with most mods here requiring at least one of the "utility" libraries (Magic, Shader, or Lazy), it's even more silly to expect Alex to not break mods using these things that, in doing so, are already outside the scope of what the engine is written to do.
