Those organisations are
not part of the Brotherhood. They are part of the Assassin Order. The Brotherhood are the Assassins who have not lost their way, who infiltrate the League of Shadows etc, trying to reform it from the inside, because the Assassin Order is far too powerful, especially with Ra's Al Ghul leading them.
Also why doesn't Rick Deckard fit? He hunts down Androids (Replicants) for a living, he would be perfect for trying to stop infiltration Terminators who've got that human skin. Not to mention he's got some combat ability.
Also Kara Thrace is from the past? Isn't Battlestar Galactica set in the future? They've got space ships and stuff? Anyway we can always cryogenically freeze her or have her travel at near light speed before crashing on Earth to explain how she ended up in the future from the past but has no way to return.
So instead of Doomsday we got Godzilla? I can dig it!
Everything else sounds cool to me.
I should have asked for settings you wanted to have in the setting. Because the only way I can think to get Elder Scrolls to fit in Fusionfall that keeps you happy is to do a
Once upon a Time thing where the Elder Scroll characters are from another realm but due to a curse or some other act of reality shattering (like, the sleeping being who dreams Elder Scrolls wakes up) are brought to the Fusionverse. Then the Fusionverse changes as the Elder Scrolls elements slowly start altering the 'real world'.
I don't know, it's tricky. A lot of these settings in this world are going to be cameos regardless. There's just too many otherwise.