Okay, here's my theory: Shovel Knight was added as a replacement for a more iconic 3rd party who Nintendo didn't get the rights to.
Let me explain via timeline:
- December 2014: Nintendo decided the DLC plans for Super Smash Bros. Roy and Lucas were chosen. They decided on three third-parties, Cloud Strife, Ryu, and one other.
Capcom was already working with Nintendo on Smash Bros., so they started developing Ryu first.
- May 2015 - Pre-emptive files for Ryu and Roy were added to the game along with placeholder files for the other third-parties, and found by dataminers.
- June 2015 - Ryu, Roy, and Lucas finished development and were released mid-June. Cloud now started development. However, the last third-party couldn't be obtained, so Nintendo looked for a replacement.
- June 2015 - Nintendo looked at social media and the recently opened Fighter Ballot and saw demand for Shovel Knight. Since the game was a recent hit and was getting exclusive content on Nintendo, including amiibo compatibility, Sakurai approached Yacht Club Games, his creators, for permission to use the character.
Due to YCG being amicable with the use of Shovel Knight IP, being friendly with Nintendo, AND a small indie dev, they agreed to him instantly. Shovel Knight started development alongside Cloud.
- August 2015 - Inklings were selected to be DLC for Smash Bros. due to their immense popularity. Development begins.
Shovel Knight is leaked.
- September 2015 - Inklings placeholder file is added to Smash Bros.'s internal file, however none of the files are named due to the datamining of Ryu and Roy.
- November 2015 - Cloud is officially revealed.
With the bulk of DLC finished, Wolf starts development.
- December 2015 - Cloud and Shovel Knight are released.
- 2016 - Inklings and Wolf are released in the final patch of the game.
FYI, the replaced 3rd party I have in mind is Solid Snake. He would have been decided in December or January due to his popularity and status, but after the controversies surrounding Konami in 2015, including the rumoured departure of Hideo Kojima (Snake's creator) from the company, Nintendo decided not to get involved and choose someone else.
The only thing this theory doesn't address is why Nintendo didn't simply choose one of their own characters. What could have happened is, they looked at ALL the Ballot results, and of all the most voted, Shovel Knight was chosen due to Sakurai seeing value in adding an "indie" rep and due to his potential as a fighter.
This all seems crazy, but that's just a theory.
A Game Theory! Thanks for reading!