While the structure of the different sectors remains mostly the same, there are some differences:
Keycards
The number of keycards you can earn may differ per sector. The more keycards you earn, the closer you are to your next reward.
Data Disk Stockpiles
Different sectors may have different Data Disks available as rewards, though some may repeat.
Enemy difficulty
Just like Easy, Normal, and Hard, subsequent sectors provide increasing difficulty by raising enemy levels and adding additional/more powerful Modifiers.