The Metroidvania style indie-game Axiom Verge was very close to having a secret Samus Aran costume in the final game. In an AMA with creator Tom Happ and business dev Dan Adelman, it was revealed that the idea of including a secret Samus suit for protagonist Trace to wear was pitched to Nintendo.
The suit was intended to be a reference to the original Metroid Justin Bailey passcode, which took Samus out of her Varia suit and into a magenta leotard. Adelman explained that Nintendo did not grant them the permission to include the suit despite initially liking the idea. Remnants of this idea remain in the final game with a Justin Bailey passcode costume change of their own.
Despite Nintendo denying permission for Samus Aran’s suit to appear in Axiom Verge, Adelman claims that they have always been very supportive of the game and continues to express their enthusiasm.
You can view the entire AMA here.