Black Rutile's origins.
Despite being one of the evilest characters in the series. We know very little about how she turned out this way. It is heavily implied that she was once a genuinely nice person, so, what caused her to change?- It's implied in "Made Me Realize" by Pink Diamond that Black Rutile simply let the power White Diamond gave her go to her head.
Other sapient aliens
According to Rebecca Sugar, sapient life forms were something that was very uncommon, if not, rare to come by for the Gem species. In the newest installment, we see that these sapient lifeforms aren't as rare as we thought they were. Why was this never brought up in the original series? Did some of the gems know about the existence of these other beings, and choose to keep their existence a secret in order to protect humanity from putting themselves in danger? Who knows? Mother of Pearls
We learn that there is a gem known as Nacre that is a powerful gem known to be the first pearl and is able to create Pearls of her own. But the only being we have seen that has been able to create pearls is...Shell. Could it be that Shell is actually Nacre imprisoned trapped within the Reef? If so, then it means that the longer a gem stays in an object, the greater it is for them to lose themselves and are reduced to simple machines. This explains why gems such as Desert Glass act erratically even though they aren't corrupted. Perhaps in Lapis Lazuli's case, maybe the reason her mind wasn't completely assimilated into the mirror wasn't because of her willpower, but rather because her gemstone was cracked, and that crack was severing her assimilation into the mirror she was trapped in. The Magmen and the Metals
These two silicon lifeforms are very similar to gems in that they are almost human-like in appearance, can shapeshift, are able to summon weapons, and can control the elements. Is it possible that all three of them are a part of the same family?