Wow. Just wow. Before Crusade this worked great: I had a mod developed, that I spent a fair amount of time working on btw, that was just like a mod you'd put in the User folder, but you copied it directly into the game's actual installed files instead.
This allowed us to bypass all the BS Stardock-imposed restrictions on Multiplayer, except MegaEvents being off (grr) and no random AI races (grr). I had a large number of Custom Factions designed, and was even able to swap the XML values around to get Insane map size working in Multiplayer (THANK GOODNESS).
Except with Crusade, I can't get Custom Factions to show up when made with .faction files unless I put them in the User folder, AND I can't get Custom Factions to show up when made with a FactionDefs.xml file unless I put them in an actual "Mod" in the User folder. And guess what: BOTH methods are now disabled in Multiplayer.
My ONLY working option for getting the game setup the way WE want it, is now gone. Congratulations StarDock, you just ruined the whole thing for us. (Not that Crusade is playable anyway in its current state by the sounds of things, sigh.)
I'm now going to uninstall Crusade, and HOPE/PRAY that you guys didn't disable additions to the root installed FactionDefs.xml file in the BASE game too with your update, b/c otherwise we won't even be able to play at all...