Loads of ways. Is X supposed to be able to hit something of height Y? Archers might be able to hit, but meleers cannot hit high flying things. How does "fly over the melee front and attack the mages in the back" sound like a strategic change to you?
Not to mention new ways to cross maps. If you fly you might just hit all those vital trigger thingies nicely planted to make the story work out? Do they have to make MASSIVE trigger zones? wouldn't that allow far more errors if hit wrong (which can be easier if there is more to hit)?
Besides that I have no idea how jumping could alter combat... or add anything but uselessness... And uselessness is usually seen as a bad thing, no?