Height should not confer Disadvantage to hit a creature, nor that creature Advantage to hit you.
While an argument can be made that height should confer *an* advantage, granting *advantage* is too powerful in how much it unbalances the system the game is built on. Even basic flying enemies become unfun to fight as you spend turn after turn missing. This vastly reduces the power level of certain classes, and radically changes the dynamic on certain spells. A whole party of wizards with Magic Missile becomes considerably better at ranged combat than a whole party of sharpshooting rangers with Archery
To put this in perspective to players who don't understand the system, two EQUALLY MATCHED CREATURES, when separated by a few feet of height in Baldur's Gate 3, give the elevated creature a 3:1 advantage! This means that if you thought we would ever be capable of fighting a dragon in Baldur's Gate 3, you are sorely mistaken, unless they simply don't fly.
This might make sense in a game like Divinity, where every class has incredible mobility, but few classes in BG (even with Jump) have mobility like that. The system that you are using for this game is NOT DESIGNED for the mechanical equivalent of invisibility to be granted with a small height increase.
We can see in this screenshot, a Spectator that is 20 feet away, and obviously above me, I have a 36% chance to hit it as a level 4 character with 18 charisma. A Spectator is a CR3 creature (so this should be an easy encounter) which has the Armor Class of 14, so I should have a high chance to hit it, but instead I have ~35% chance to hit it. To put this in perspective, this is the *same* chance this character would have to hit an Iron Golem, a CR *16* creature that is NOTABLE for having a high armor class.
I would like to point out that with NO mechanical advantage to height, the enemy still has a substantial advantage in terms of positioning, denying cover to the lower combatants, denying combat to high-damage melee opponents, and ability to reposition. To put it bluntly: Height also provides a hell of an advantage without mechanically doing the same thing being unseen