Eeeee! I've been waiting for this stuff for sooo looong. :D It's amazing to start actually getting it set up, and amazing to lift the veil off of some of what is on the way. And as always, we have Schema to thank for making all these things happen.
The way I see it, StarMade is one of the most amazing games I have ever played in almost every area except when it comes to actually
doing something. Now we're adding in things to do. There will be so much more
reason to play, with so many more things to accomplish and events to deal with. This is only the beginning. This is quite a bit like the move from Minecraft Classic to the survival Minecraft that took the world by storm. (Though this won't make StarMade any less of an amazing platform to just build ships and stations in for those who just want that.)
I personally lean towards singleplayer, and the effects of these new faction mechanics will obviously impact multiplayer long before singleplayer simply because players on servers can make the most of it right away. Singleplayer requires a sufficiently complex AI enemy designed to understand the system. But I don't mind a little waiting. The future is bright.
I don't think the name that Aceface used was really the point at all, I think they were just trying to say that it would be interesting if there was a bit of back story behind the concept of faction points. The idea of lore isn't complicated unless you get confused by integrating story into your game. "flux crystals" was just a cool sounding name, if anything your attention to only half of an uncomplicated suggestion is what is unrelated.
Don't worry, lore is taken into consideration. However, gameplay always comes first. (Not true in all games, especially atmospheric ones, but true for StarMade.) "Faction points" is something that makes sense and can be understood quickly, and that is more important than the backstory players will not be reading while being killed and losing faction points.
Besides, the term "faction points" could actually be made part of the lore, it would just need to be written right. Perhaps it would be something like colloquial slang for the cumulative resources a faction has, physical or otherwise, but specifically referring to the way it ties into galactic politics when in action. Or maybe it refers to the system people prefer to use when trying to quantify something abstract like faction power and display it in numerical form. (Tallying "points" based on a variety of factors that relate to faction power.) Don't worry; it won't be left a giant loose end. It could be one of two terms used for roughly the same thing, with the other being something more solid and lore-bound. (And "factions points" as slang used for the reasons I mentioned earlier in this paragraph.)
EDIT:
Throwing random name in : Cubatoms XD (as that system is now wrecked iirc, the name is free to use, right ?)
You collect Cubatoms and spend Cubatoms for your faction.
Cubatoms are by no means gone from the StarMade lore. Their existence as the fundamental particles that create the universe remains. Actually, the Fabricator's ability to carry large amounts of potential matter relates to the behavior and physics of Cubatoms.
(I love dropping little hints and bits of lore.)