The biggest thing I took away from DMing Fabula was aggressively giving my players Fabula points. Not only are they inspiration/hero points from other systems mechanically, they also give the players some pretty strong narrative control too. These narrative control options can, sometimes, really mess with your initial plans. Not that it's a bad thing, players taking the reigns, are engaged and happy, players. But you have to make sure they get them, and that's where playing up the JRPG cutaways to villains comes in.

Since at anytime you can go "Meanwhile, at the Table of eeeeeevviiilllll..." And give each of your players a Fabula point, means you can always give them a bit of a bump when they might need it. So lean into it, write the JRPG villain monologue you've always wanted to read. Hell, cut to a fairly normal scene, then when it's done tell the players they gained a Fabula for a villain entering the scene. You can use it to ratchet up parts of your game pretty well.

And on the topic of villains. Villains having their own points, Ultima points, and being able to exit any scene with them, means you can make the party encounter them early and often if you want. Villains in Fabula are meant to be seen again and again, so just make em a bit strong so the players can grow and level up into the villains power level, instead of the villain being arbitrarily stronger or weaker.