For the universe, keep the pendulum swinging, even if the major actors change.
For example, imagine the BT map on a spinning top, with one part rising higher at times, before dipping in turn as other parts of the top's rim rise above the others. That dynamic of a slightly unbalanced top, which has one area higher than the others, but changes what part is in the ascendent over time, is critical to both a dynamic universe but also a contained universe.
To further the analogy, when to much weight (power) is invested in the center over prolonged periods, the whole thing slows down and peace breaks out, as Terran influence causes friction and slows the spinning.
So therefore, even if the factions we might barrack for fall, others will arise and keep the spinning going and in their own time rise and fall.
I would maintain this spinning balance, avoid great Terran powers, expect for eras of peace, and create new and interesting themes in existing factions or, where necessary, raise new factions that have there own strange flaws, interesting twists, cultural bias and characters of interest.
I would also make sure the visual aesthetics of the universe both advanced, but always maintained connection to older eras, gaining the benefit of both. I would look to support the main game, as that is the foundation upon which all was built, but also expand items like Alpha Strike as a simple doorway into the broader universe, where more detail and good fiction help the gamer expand their investment and involvement.
I would also wipe out one world each year, completely at random, just to set people off.