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Well, we could follow the site's canon and say that perma-fusions, after a while, lose their individuality and become one. Thus, this would enable them to take on a more regular-gem appearance if wanted to.
In my opinion, it could also be a cause from regeneration. Garnet may have taken enough damage to where she regenerated in her own image, thus ditching extra arms and legs.
Or, it could be a product of what kind of gems were fused. More powerful or rare gems could cause more powerful fusions that would include the extra limbs and what not. Ruby is a common soldier, therefore not rare or very powerful like Jasper would be. Sapphire is a rare gem, however she was combined with a common soldier. The pair makes a powerful fusion, but not a fusion that can call for extra limbs.
Another answer could be that they are both smol gems, and two smol gems fused together could create a normal-looking gem.
There could possible be a dozen more answers, but these are the ones I can think of. Since it has not been explained in the canon in any way, it's more of a "pick your guess" and "make a headcanon" type of thing until proven wrong.
I like to think that a fusion takes on a more human like figure the more the two gems who are fusing are in sync. Malachite was very monstrous because lapis and jasper didn't have compatible personalities and were so unstable, however a gem like garnet, where the two gems fusing get along great, takes on a more human like form since it is so stable
Officially the Crew explained that it was basically Rule of cool but there are some other head-cannons that show some patterns.
The main idea i have seen is that Gems have multiple eyes when they have different goals in mind or 'don't see eye to eye'
and gems have multiple arms when they have different fighting styles. Opal 2 Eyes, 4 arms: Opal is only created when Amethyst and Pearl have a shared Goal in mind (saving Steven,Firing at the ship, ect), thus she only has one set of eyes. Amethyst and Pearl also have very different fighting styles,thus the multiple hands.
Sugalite 5 Eyes,4 arms: Garnet and Amethyst also fuse for different reasons aswell,remembering that Amethyst sees forming Sugalite as a method to make her feel stronger.While Garnet does it for the mission. She also has multiple limbs cause Garnet and Amethyst have different fighting styles aswell,Garnet uses strong punches while Amethyst is more out of control and unplanned with her style.
Sardonyx 4 eyes,4 arms: Cause Pearl was fusing for very different reasons than Garnet aswell in this, and yet again Pearl and Garnet have different fighting Styles.
Alexandrite ? Eyes, 6 arms: Similar idea to the above,different fighting style,set of arms for each and we don't know how many eyes they have
Rainbow Quartz: 4 eyes 2 arms: Rose and Pearl are also fusing for different reasons aswell, but they have two arms cause Pearl and Roses fighting styles are very similar (Rose did teach Pearl how to sword fight).
Garnet: 3 eyes 2 arms: Sapphire and Ruby are very in sync but don't always see eye to eye due to the opposing personalties. They most likely fight in a similar style though as both of them must have some sort of hand based weapon, since how else would they form the Gauntlets.
Malachite 4 eyes 6 arms: Same idea as the rest,except Malachite lack of legs may be a play on their fusion motivation having 'no legs to stand on'.
This Roleplay is a prequel to Steven Universe to an extent with some slight retconing and its own progression to the story that will turn out differently to how stuff plays out in the show.Thanks to the message by Rose Quartz several gems are rising up to protect Earth and have labelled themselves as the Crystal Gems. Others on earth are remaining aligned to Homeworld though despite the isolation of Earth from Homeworld
All gems on earth are still stranded, the communication hub is still offline and all the space warps are shattered, it has now been revealed that this is the work of Rose Quartz and her small group known as the Crystal gems. They have rebelled against Homeworld and have chosen to protect the Earth (Trapping themselves on Homeworld to keep the warps down).
Now both sides are fighting among themselves along with fighting against the 'Corruption' a virus is infecting many gems turning most of them into mindless monsters, but those with a stronger will seem to becoming something more sinister.
The Game has changed now. The question has finally been posed, are you against Homeworld or allied with them. Or do you have your own agenda that may or may not been assisted by the ‘Corruption’. Regardless the seeds have been placed down and although it is only the beginning the fight for or against Earth and the corruption has begun. The choice is yours for how it is shaped on the Original Steven Universe Roleplay Site.
Orginal Opening Plot Here Thread That Changed Everything
Differances Between the Roleplay and the Show
*Thanks to Rose Quartz' message the Gems on Earth are entirely aware that the Homeworld Gems intend to wipe out the human race.
*The "corruption" is being treated like a virus due to lack of info about it on the show.
*Garnet, Pearl and Rose are assumed capture on Homeworld
*Garnet,Pearl and Rose broke the space warps to delay Homeworld
*Thanks to Roses Message gems now know what the Kindergarten was used for