Wouldn't it be a great idea to have the fate of the Ark determined by who wins the weekly war more than the opposition within say a year or two.
I think it should be up to the players to determine how the sequel (if there will be a sequel) storyline plays out.

Wouldn't it be cool to feel like you were involved in something much bigger than yourself?
That you determined the the fate of many?

Not really because the way it is now the future story would be that resistance pwn all the ARK becomes a hell hole of anarchy and burns to the ground zombie apocalypse style not very conducive to a sequel.

"bigger than yourself" is the new self. Up your expectations of size and power.

Security should win, therefore there would still be conflict and a more dire situation for a sequel.
If Resistance wins, well, everyone dies or is blown up.

...So, no. Not really.