While it may have set the tone for the entire series here's why the Steven Universe pilot isn't part of the show's canon. The Cartoon Network series follows the colorful, cosmic adventures of the title character, a young boy who lives in Beach City with an alien race known as the Crystal Gems. Steven is half-gem himself and the show follows him as he learns to use his powers to help defend his home town from assorted alien threats.
Steven Universe has been praised as both a fun adventure series and for taking on mature themes and issues. The show is also remembered for its insanely catchy musical numbers. Season 5 finale "Change Your Mind" appeared to act as something of a finale to the show and Steven Universe season 6 has yet to be confirmed. Fans of the series don't have to worry just yet as Steven Universe: The Movie will air sometime in Fall 2019.
What some fans may not realize is that a short, seven-minute pilot was created to pitch the concept to Cartoon Network by creator Rebecca Love (Adventure Time). The Steven Universe pilot - which is also known as "That Time Thing" - quickly set up the concept, with Steven begging the Crystal Gems to take him on an adventure. They refuse since he's too young, though Amethyst secretly gives him a magic hourglass to play with. He winds up using it to insult a Big Donut employee, which creates unforeseen problems with the timeline and it's up to him to fix his own mess.
The Steven Universe pilot is a short, energetic episode that lay the groundwork for the series to later build on. It's not essential to have seen the pilot, however, with the showrunners later confirming it isn't intended to be canon. The characters were later slightly redesigned from their pilot looks with Pearl, in particular, having a different costume and hairstyle. The show did reuse some elements from the Steven Universe pilot, with the magic hourglass later appearing in "Steven and the Stevens" from season 1.
The pilot essentially functioned in the same way as the 1991 promo that was created for Batman: The Animated Series when it was being pitched to Fox. They both set up the tone and feel of the show, but they were never intended to actually be part of the series itself. The Steven Universe pilot is still a fun curio for those who love the series and works perfectly as an introduction to the world of the show.