To the Stars/WMG

Ryouko's magical girl outfit is specifically intended to look like Madoka's.
Not her goddess outfit, but Madoka's original pink and white uniform. Maybe the author wants them to look alike for thematic reasons. Maybe there's an in-universe justification for it, like Ryouko is descended from Madoka's brother or something. But don't all these features sound familiar? The magical girl in purple from chapter 5 also has buttons, a lacy dress, a soul gem at the base of her neck, and a bow. If the similarity between Ryouko and Madoka is intentional, then whatever is causing it probably applies to this girl as well.
 * Lacy dress goes from chest to calves.
 * Flares out and ruffles at the bottom.
 * Sleeves flare out and ruffle.
 * Buttons on the chest.
 * Soul gem at the base of her neck, on the front.
 * Weapon is a bow.

Also, Ryouko mentions in chapter 9, during her vision, that the Goddess looks familiar. Perhaps regular Madoka is familiar to her as well, and Ryouko is subconsciously mimicking her? Or perhaps any similarity to Madoka is a coincidence and Ryouko only resembles the purple magical girl, due to hero worship or a family connection or something.

Ryouko is the indirect descendent of either Sayaka or Madoka.
In the second chapter, Mami notes that when she saw Ryouko the system should have flagged the relationship she has to someone from far in the past. Mami felt relief that the computer didn't know things from so far back and that "she had found herself looking at a face she hadn't seen in a long, long time.". This would indicate someone from the original show.

Hitomi or Kyosuke's descendents wouldn't flag high on Mami's radar and while Ryouko has the same last name as Hitomi any of Hitomi's children would have the father's last name, Kyouko's still around, and Homura disappeared without descendents. If she had any, the Cult of Hope would have incorporated their entire line into the church already. This leaves Sayaka, who may have cousins or the like or her parents had another child, or Madoka, who Mami does not know but who did have a living brother. Homura may have mentioned Madoka's family at one point and dragged Mami and Kyouko to see them on occasion.

The mention in-fic about the ability to become a magical girl running in families also helps to support this idea. The aching feeling of familiarity Ryouko felt could have either been a feeling all magical girls have for Madoka or the feeling of meeting a long-lost relative who was dearly close before vanishing.

Hitomi became a magical girl and had children, making her the ancestor of Ryouko.
In the opposite direction of my other guess, Hitomi is Ryouko's ancestor. Nearly as old as the others, it would be a surprise to anyone that she's still kicking at her age. Having previously been Madoka's friend and having a similar personality as her, it wouldn't be too much of a surprise for them to have similar powers and outfits. Their previous connection would make her a good person for Madoka to use for manipulating their plane.

Simona is a Honey Trap sent by the Black Hearts to recruit Ryouko.
Why? Because of Ryouko's parents. She intentionally finds potential magical girls who need a push and who are very likely to be powerful. By getting close to them and exposing them to demons, potentially powerful but purposely sheltered magical girls can be awakened and entered into the corps away from interfering forces, this one being Ryouko's parents. Simona goes from place to place to fulfill her role and recruit as many girls as possible.

The missing magical girls are being used as guinea pigs in a misguided attempt to learn how to prevent girls from dying of corruption.
If you don't believe Homura and Kyouko, then you would probably think that disappearing after soul gem corruption is a natural magical process without any guiding intelligence. But Homura seems to provide evidence that soul gem corruption doesn't need to be fatal. And truthfully, it shouldn't be. Perhaps anyone with a sufficient understanding of magic could realize that girls whose soul gems are blackened don't need to disappear to another plane. Clearly, the next step is to research how to extend Homura's case to everyone. If technology can stop aging, the natural death of all humans, why not stop corruption, the natural death of all magical girls? Of course, Homura is the only one for whom living with such great soul gem corruption doesn't mean a fall into despair and the birth of a new witch. So to the frustration and befuddlement of those who don't believe, every attempt to extend the lifespan of girls with black soul gems would end in their mysterious disappearance (into Madoka's arms). But surely they're on the verge of getting it!

This explains why Madoka is getting personally involved. Her wish has helped behind the scenes, but this affront to her nature needs direct intervention. Resolving it requires someone who believes in her and can understand why forcing girls to stay alive with corrupt soul gems is a bad idea. Poison Oak Epileptic Trees bonus: Yuma is involved in this but is keeping it a secret because she knows Kyouko would flip shit.