Final Fantasy VII Remake will take up Square Enix's time for the next few years, but it's possible that the game derailed plans for another sequel that took place after Dirge of Cerberus.
Final Fantasy VII has two sequels in the form of Advent Children and Dirge of Cerberus. Advent Children resolved a lot of the dangling plot threads from the original game, while Dirge of Cerberus added a bunch of new ones. On the Way to a Smile (a spin-0ff novel set between the events of Final Fantasy VII and Advent Children) also added elements that opened the door for more sequels, including ways to keep characters around for years after Advent Children ended the story of Cloud Strife on a happy note.
The secret ending to Dirge of Cerberus created a huge sequel hook and On the Way to a Smile created possibilities that could keep the story of Final Fantasy VII going for years. Whatever plans were in place seem to have been supplanted by Final Fantasy VII Remake, so what exactly was Square Enix setting up?
Genesis Returns
Genesis was a major character in Crisis Core, but he is taken in by Deepground at the end of the game and is missing throughout the events of Final Fantasy VII. It's revealed in the secret ending of Dirge of Cerberus that Genesis is still alive. He claims the body of Weiss the Immaculate, says that it's not the time for slumber and that they still have work to do. Genesis flies off with Weiss' body... and that's it. Barring the Final Fantasy VII post-credits scene, this is the last moment in the Final Fantasy VII timeline.
According to the Crisis Core Complete Guide (via the Final Fantasy Wiki), Genesis has returned to protect the planet, but from what? All of the threats have been defeated at this point, with Jenova, Sephiroth, Kadaj & his cronies, Geostigma, the Weapons, and Deepground all gone. What is Genesis protecting the world from and why does he need Weiss' help?
Red XIII & Vincent's Pact
At the end of Final Fantasy VII, Red XIII is shown traveling to the ruins of Midgar with his children. This is 500 years after the events of the game, so fans were unsure whether humanity survived the Holy/Meteor crash until the events of the spin-off games and Advent Children.
The novel On the Way to a Smile confirmed that Vincent is effectively immortal, as his body has practically stopped aging as a result of the experiments performed on him. Red XIII belongs to a long-lived race and he goes through a crisis when he realizes that the day will come when all of his friends are dead. Vincent and Red XIII make a pact to meet once a year in Midgar for as long as they still live.
Vincent was always a popular character in Final Fantasy VII, proven by the fact that he starred in his own spin-off game. Advent Children ended Cloud's story, but Vincent could have been planned to carry the franchise going forward. The lukewarm reception to Dirge of Cerberus might have killed these plans, which is why the next title was a prequel game that dealt with content directly related to Final Fantasy VII.
Both Cannot Die While The Other Survives
Sephiroth was able to return to life in Advent Children thanks to the actions of Kadaj and some Jenova cells. Cloud is able to defeat him for a second time, but Sephiroth is a very hard guy to kill.
In the world of Final Fantasy VII, beings who die return to the Lifestream within the world and are reincarnated, as is the course of nature. Sephiroth is technically not of the planet, as he had Jenova cells inserted into the body while still in the womb. On the Way to a Smile confirmed that he could maintain his consciousness in the Lifestream, so he could resist being reborn. It's also established that he will continue to exist for as long as Cloud remembers him.
This leaves the door open for Sephiroth to return in the future, as all it takes is a body and some Jenova cells. It's possible that the writers were leaving the door open for Sephiroth to come back, even after his defeat in Advent Children. Was there going to be another Sephiroth comeback? Was this the crisis that Genesis returned to stop? No one knows and the fans are only likely to find out if a Final Fantasy VII Remake sequel is released that keeps the spin-offs canon.
Square Enix opened the door for Final Fantasy sequels with Final Fantasy X-2, leading to Final Fantasy XIII-2, Lightning Returns, and Final Fantasy IV: The After Years. It's odd that we never saw a Final Fantasy VII-2, even though Square Enix planted lots of seeds that could make it happen. We might see a Final Fantasy VII Remake sequel, but who knows what form that could take with the altered story of the remake?
Final Fantasy VII Remake will be released for PlayStation 4 on April 10, 2020.
Source: Final Fantasy Wiki