Well, Here's how I'd see X9 in terms of gameplay, visuals, story, and characters:
Character Revisions(gameplay-wise, visually, and plot wise):
X: X should get back the Hover skill he lost after X5, along with the armors from X5. Visually, his design should be made to fit Z1-3. Gameplay wise, his controls should be based on balanced power and good effieciency.
Zero: Zero should get a redesign to fit the Z-Series. Next, instead of all the varied weapons that you got in X8(such as that hammer, the knux, and spear thing), Zero's going back to his saber, his buster, and a series of Shotokan moves. Also, the Z-Virus should play an addition to gameplay. After his bad ending corruption in X5, he should be able to use it to his advantage, meaning that it strenghens his offense at a cost of defense, like in X5.
Axl: First off, Axl should be changed from a ranged fighter to a magic user. His gameplay style will be more oriented for those that like to take things slow and easy. He'll learn several spells like waves of fire. Also, in terms of plot, Axl will be temporarily unavailable for the purpose of that, which I will now explain.
Next up, we have Plot:
My plot would take place about a month prior to the events of X8. Sigma, believed to be dead, pulls another Sigma and comes back, this time in a demonic-looking version of his eldest form. He now has a space station, but he is not attacking the Earth, as he did with Eurasia, however he now is planning to use it to take over the satellite system of Earth and transmit a new, superpowerful version of the Sigma Virus!
He decides to try it out on a construction site, which is beginning construction on what will be Neo Arcadia. The message recieved, the Hunters move out to the site, and after clearing the site's threats, finds a new foe has risen; OMEGA. It seems that Sigma has enlisted this maverich to end the Hunters for good. Testing their abilities, Sigma opens up 8 sets of coordinates, which go to the 8 stations of his base, which hold 8 mavericks. One maverick down, and Axl is feeling somewhat ill. X and Zero ask if he is okay, and Axl replies he will be fine for now. 3 more Mavericks and Axl succumbs to a temporary corruption. The hunters do not know what is making him go maverich, but reccomend X and Zero to go to where Axl ran off, neutrilize him, and bring him back to the base. Afterwards, they find that it is caused to what Lumine did to him a month ago. Alia says that she, along with Layer and Pallette, will be able to cure him, but they'll need time (about 4 more mavericks). After the final 4 are taken down, Sigma congratulates them, and opens up the coordinates to Sigma's Lair. Omega returns once again, and after his defeat, dissapears. While X is fighting fit, Axl is damaged severely and returns back to base. Being alone, Sigma challenges X and Zero for the final time. Prior to his final fall, They find that Lumine is still alive, and was using Omega as a vessal to stay alive. Lumine wishes to finish what he started, and challenges X and Zero. After his first form is beaten, Lumine strikes down X and Zero temporarily. Just as they were about to be done in, Axl returns and wants to get revenge on Lumine. Lumine obliges and becomes an even stronger form of Omega, the form that is referenced in the Elf Wars and in Zero 3. After Axl halves Lumine's health, he says he is not able to help any further, as he's expended his stamina, leaving Zero and X to finish the fight. After Lumine's final defeat, his reploid spirit floats off as a purple and white spectere, but then purifies. He apologizes for what happened in X8, because despite his claim that the Next-Gen Reploids were immune to being infected by the Sigma virus, they were not, and were still able to go Maverick, and he himself succame to this. Saying this, he fades away. After this battle, Axl decides to leave the hunters and fight for justice as a solo act, Zero is put into stasis, and X becomes ruler of Neo Arcadia, thus leading into the events of Zero 1...