The JJBA manga is indeed finished. It had a great journey and wrapped up with a satisfying conclusion for fans. However, there's always the possibility of spin-offs or related works in the future.
One idea could be that Kira Yoshikage from JJBA somehow ends up in the Naruto world. Maybe his Stand ability could be misinterpreted as some kind of strange ninja jutsu. He might try to live his quiet life there, but his actions would surely draw the attention of the ninja. For example, if he starts using his Stand to kill people in the ninja villages, it would be like a new and unknown threat to the ninja, and they would have to figure out how to deal with it.
One interesting JJBA x MLP fanfiction could be where the Stand abilities from JJBA are introduced into the world of MLP. For example, a pony might gain a Stand that gives it unique powers, like the ability to control time in a small area, similar to DIO's The World. This could lead to all sorts of adventures and challenges within the pony world as they figure out how to use these new powers and face off against villains who also might get their hands on Stand - like abilities.
First, decide on the starting point. If you start in the JJBA world with Kira Yoshikage, you could have him accidentally open a portal to the Naruto world. His confusion and his instinct to keep his murderous habits hidden would drive the initial plot. He might try to blend in, but his different appearance and behavior would make it difficult. In the Naruto world, he could encounter Naruto and his friends who would sense something is off about him.
First, you need to decide on the main concept. Are you going to focus on bringing JJBA characters into MLP's world or vice versa? Or maybe you want to create a completely new world that combines elements of both. Then, think about how the unique aspects of each franchise will interact. For example, how will Stands work in a world full of magic like MLP? After that, start creating your characters. If you're bringing in JJBA characters, how will they look and act in the MLP universe? Sketch out a basic plot, like what the main conflict will be and how it will be resolved. Don't forget to add your own unique twists to make it stand out.
One of the descendants could be Giorno. Giorno has his Golden Experience Stand and is quite different from Jonathan in many ways. He's part of the new generation of the Joestar family. Also, Josuke could be among those he meets. Josuke is known for his Crazy Diamond Stand and his strong sense of justice, which he may have inherited in part from Jonathan.