As you collect Flags from more and more Super-Secret Bases, you will eventually increase in Rank and in turn unlock a number of things, as below.

Unlockable	How to unlock
Secret Pals can use their skills twice daily, a Confetti Ball, and Garchompite	Reach the Platinum Rank (1,000 Flags).
Secret Pals have a fourth skill, you can take photos of your Base, and Mood Lighting	Reach the Gold Rank (500 Flags).
Secret Pals have a second skill, more items in Fortree's Secret Base Store, and a Blackboard	Reach the Bronze Rank (50 Flags).
Secret Pals have a third skill, more items in Fortress's Decoration Store, and a Jukebox	Reach the Silver Rank (100 Flags).