Oh.. this is a unique type of crazy.
What you ACTUALLY means is there is RARELY an 'up' in RPG's... but that as zip to do with RPG's and everything to do with devs not creating a z-axis for their engines.
1) Once they implement the z-axis, then the devs must fill the new spaces that the player can now enter, otherwise everyone complains about there being nothing there. Plus that it looks awful. So, triple dev time and costs to cover three distinct visual areas for each space in the game.
2) Once you can fly high in the sky, melee combatants can never hit you. Ever.
3) Ranged ground combatants can only hit you if you choose to fly close enough for them to shoot you. And you can abandon combat with them at any time, because you can fly away into open space, where they can't follow.
4) If one member of the party is flying and nobody else is, then the dev has to build two separate areas for just the flyer to see and interact with, while the rest of the party twiddles their thumbs. Putting bunches of time and resources into an aspect of the game that will only be underutilized and half-baked, all so people can say - oh cool, look, I can fly; now I have to go land so I can play another portion of the game with the rest of the party. Repeat
Essentially Fly in an RPG, like most superpowers, is Easy mode. It defeats any opponent that can't also fly, it always you to safely retreat any time you want. And it instantly divorces you from the regular game content. And it does so by demanding a huge devotion of resources on the dev's part. So, lots of time and money spent on something to break the game. Yay.
Which is why the Marvel and FF games give you the power to Hover and call it Fly.