One of the biggest things that Noah received from the upgrade of the System twice was the increase of his Unit Slots from 8 to 12!
The number of terrifying Rift Bosses that he could now lead increased to an even greater amount as it allowed for his battle power and clearance of the Tower, Shattered Planes, and the Crucible to be that much easier.
One of the newly added features even had to do with the past unlocked features, where the first new feature Noah received when he broke past the 1 million Idle Exp barrier was the introduction of something called Difficulty!