Think about it this way. How many gods does humanity have? Kill the greek gods and the romans make more, kill those and the catholics make more, kill those and science becomes it's own.
Kill all the gods you want, the hive will always have another god. The Al'Akhul strike talks about him wanting to dethrone Oryx, so there is already a succession mechanic in place for the hive, biggest baddie rules.
The Fallen don't deal well with loss, hence their scavenger, disorganized nature, but I'd expect an organized house to come in from out of the system at some point and show us what they can really do.
The Vex don't have gods or identity, only function, so they will find a way to repair the loss of Atheon (like they tried with the Nexus mind) via the time stream or they will adapt around the loss. Who knows, maybe they allow this timeline to persist because they needed Atheon destroyed...
The Cabal are militaristic. They will always establish a hierarchy. The main command will promote new leaders. If we ever kill the absolute top of the cabal command they would eventually establish a new order.
So there should always be enemies to fight, we will cripple the minions of the darkness, but it will be a very long time before we "win".
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In the lore atheon and the vex with him are rogues that went against the black heart which is the god of the vex.
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Which is odd for a race made up of a homogenous fluid placed in varying amounts in different skeletons.
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You raise some very good points.