How about this. The beasts that you fight, and the ones you kill, are only lesser beasts. Still massive and towering, though only a few heads taller than a super mutant behemoth, or a mirelurk queen. (Whichever one is bigger). Over time, you grow comfortable in fighting these giants. Ten or so shots from your trusty fat man and down they go.
But in the late game, when you're deep rooted in your chosen faction, something wakes up. A titanic beast, larger than Liberty Prime, by at least a head. The creature reeks havoc upon the wastelands. It is up to you, and whatever faction you have chosen, to throw everything you have at it. Lets use the BoS for an example.
As soon as the monster shows itself, Liberty Prime is sent out to fight the monster, but is ultimately defeated. It is clear to the brotherhood that if this creature is to be killed, Liberty Prime requires a number of upgrades before he can even dream of fighting this creature again.
So you're sent on an advanced fetch quest to gather the needed parts and components. You notice that attacks from the lesser beast become far more frequent than before. Entire settlements and villages have been leveled by the increased kaiju population, and the great beast itself. Whenever the supreme monster decides to show itself in your general location, you have no other option but to duck your head and hide, and wait for it to leave.
After getting everything you need, Liberty Prime is upgraded to the max, with enhanced fighting skills, a more advanced a.i and processor, stronger motors and hydraulic. Even getting a considerable size boost. The robot and the monster do battle, and Liberty Prime emerges victorious. The entire wasteland is left in nearly total ruin. Nearly as bad as right after the great war. From coast to coast, the creature had devastated all.
So, at the end game, the faction you've chosen, takes advantage of the wasteland's weakened state, and seizes control. They quickly destroy the other factions and rebuild the wastelands.