I don't like that they didn't show anything leaning towards the Black Mages finding a way to live. That's about the only thing I would change.

Picture this, Lindblum (after the seen with Garnet and Zidane embracing), Vivi is shaking hands with Cid, after he turned back to his normal self of course, and and walks out to the balcony (or returns to the Black Mage village, whichever you think is better) and addresses a crowd. Camera pans out to reveal the town square filled with Black Mages. He gives his speech and the crowd of Mages goes wild. Cut to the scene of the Mage manufacturing plant under Dali. A new machine has arrived and the Mages are being lined up before it. The first gives Vivi and Cid the thumbs up before going through. Vivi and Cid await anxiously on the other side for the results. When the Mage comes out the other side he comes out standing straight up, like the robot he used to be. A few seconds go by before life springs into him. He checks himself and gives the pair of onlookers another thumbs up, signifying success. Cut to scene where all Mages are being carted through the new machine. Fin~

Or

Vivi returns to the Black Mage village directly after shaking hands with Cid (no balcony scene) and walks to the center of the village. All the Black Mages come out of their huts and head over to where he is, surrounding him. Close in on his face and follow his hands up to show him holding a miracle cure in them. In turn all the onlooking Mages thro their hands up in ecstasy!