Hi UltraUberPieMan
The Engine does save a lot of data, but much of it is backups for your protection. If you feel comfortable that you no longer need the backup data, you are welcome to remove it.
As Paul mentioned, there are backup maps in your project’s Saved/Backup folder. Depending on your settings, you can also have backup assets saved.
The Launcher stores project backups in Unreal Engine/Launcher/Backup.
When you download sample content, it is initially downloaded to your Vault in Unreal Engine/Launcher/VaultCache. When you work with the projects you make copies of them from the Vault, but if you have decided that you no longer need the Vault download, you can remove it.
And also, when you upgrade from one engine version to another (for instance 4.2 to 4.3) remember that you are still keeping 4.2 in its entirety and adding a whole new instance for 4.3. Once you are positive that your project works on 4.3 and you no longer have a need for 4.2, you are welcome to remove it if you choose.
I hope this helps, and we welcome your feedback.