It's generally agreed that it was hard to take Simon seriously as a villain. Because of this, some fans wish the series went with the original idea of having a witch as the villain.
While unconfirmed, early concept art suggests the male characters would have been more prominent, which also may have been a good idea.
Hilarious in Hindsight: Characters named after gemstones? Steven Universe must be copying this gimmick. It certainly doesn't help that Steven's gem is placed in the exact same position as the Trollz (belly button) or that the powers are initially activated by glowing—meaning roughly the first two minutes of both show's pilots are nearly identical in events.
Launcher of a Thousand Ships: Topaz has been paired up with Simon, Jasper and Onyx. Ruby has also been paired with Rock, Simon and the other members of the BFFL.
Retroactive Recognition: The theme song is performed by The Valli Girls. Two members from that band would eventually form HAIM.
On the website there is mention of Black Amber, implied to be very bad stuff, and how it contributed to how things turned out—Simon was said to have unleashed it, almost destroying the planet. It's never mentioned in the show.