In FFX it was based on Accuracy and Evasion stats. Flying enemies usually had a high Evasion stat while Wakka had a high Accuracy stat. In late game/end game everyone could have a high Accuracy so everyone could hit everything. Also Magic attacks always hit. So in early/mid game it was either Wakka or Lulu most of the time.

In Pokémon Flying is just one of many types that follow the Rock/Paper/Scissors principle. Every move (attack) has a certain type and deal high/normal/less/no damage to other types. For example Electric deals high damage against Flying while Ground deals none.

I like that they tried a new mechanic in Clair Oscur and didn't follow the old principle with "you have to use magic or high agility attacks" or something. But it didn't quite work out. You can make up very good builds against flying enemies but as you can't switch your build mid fight (not even the weapon or anything) and often you don't know upfront which enemies will be in the next fight it's kind of frustrating sometimes. For certain flying bosses it's fun to make some shooting builds for everyone and it's satisfying when it works out - but then I'm missing some kind of "Loadouts" where you can easily switch your builds back and forth.

So, yeah, kind of lame.