It's good that you're going beyond emulation! What you want to do in this case is strip BSG down to its most basic elements and abstract them, make them nonspecific. And that's what you're doing! You've got the Enemy - include a Worldship, emphasise scarcity, emphasise politics (Resulting from scarcity), emphasise flight from an old world whose spirit remains with the people and is invoked for all kinds of purposes - to produce a sense of home, to advance a political agenda, to have something to return to one day or something that is irrevocably gone.
Another quick suggestion - mandate two Fronts running at all times - one internal, relating to scarcity or political conflict, one external, relating to the Enemy.
Regarding the Agenda: The Agenda is just the stuff the MC is supposed to have in mind at all times when MCing. You can be more specific than "Make the characters' lives not boring." if you like, and I would. I like "Build towards a resolution" - how is that expressed in play? Would "Build towards a climax" be better? Consider modelling the game's storytelling structure on TV - seasons, arcs, episodes.
Regarding principles:
Create interesting dilemmas, not interesting plots (I like it! Could do with some rephrasing but the idea is solid.)
Everyone can die, but movements can endure. (I'd say "People die, movements endure" - shorter, more evocative.)
Name everyone, make everyone human. (How does this relate to the principle above? It feels like a dogma carried over from Apocalypse World, where it was a principle because the game's communities were small and . Consider the potential of including a generic faceless mass in your game. Maybe rather than naming everyone, say "Everyone has a faction" or something like that.)
Ask provocative questions and build on the answers (I like it! This should be part of every PBTA game)
Respond with challenging circumstances and occasional rewards. (This feels like a missed opportunity to emphasise scarcity - "Respond with challenging circumstances and inadequate rewards"?)
Leave the world that was lost to the players. (Not clear what this means - "Remind them of the world that was lost"? "Show traces of the world that was lost"?)
Unveil mysteries in their due course. (I feel like this would be better built into a Front mechanic)
Let the players fill in the gaps. (Covered by "Ask provocative questions and build on the answers".)
What has happened, is true. (What does this mean? It seems obvious - do you mean something like "What is done cannot be undone"?
Sprinkle evocative details everywhere (Why wouldn't you already do this?)
Make the world seem real (Why would you need to do this? It's a story! Be more specific than "real".)
Build a bigger world through play (Unclear what this means, probably covered by "Ask provocative questions and build on the answers.")
Address yourself to the characters, not the players (Generic, cool. Wherever you find a generic principle, justify it to yourself - don't just paste it from one game to another.)
Make your move, but misdirect (Generic, cool)
Make your move, but never speak its name (Generic, cool)
Think offscreen, too (Generic, cool)
Be a fan of the players’ characters (Generic, cool)