No need to care too much about flying opponents since you'll likely run a couple party members with ranged weapons anyways - Uhlan, Monk, Machinist, Archer, Time Battlemage, and of course offensive magic through the Black Mage or Red Battlemage. And I don't remember a single flying opponent tough enough to require more than one party member attacking it (maybe Garuda or Bloodwing if you're underleveled for them).

Something very important to keep in mind with gambits though is that they won't activate if the game deems the action pointless even if the condition is fulfilled.

Ally: any - Phoenix Down

will ONLY activate on KO'd party members anyways. So no need to go out of your way to buy and set up Ally: KO instead. Also you can have this gambit on all of your party members, they will coordinate and won't use more than 1 Phoenix Down per downed party member. However, if you have a White Mage you may want to turn everyone else's revival gambits to the White Mage only so you don't waste Phoenix Downs and just let the White Mage's revive everyone else with the Raise spell.

Oh, my personal favorite attacking gambit is

Foe: Lowest HP - Attack

I don't remember a single part in the entire game where I'd rather go against it. But if there is, you can always just turn off gambits and set your target manually, or put a "Foe: Party leader's target - Attack" gambit on higher priority.

Late in the game I'm also always a fan of

Ally: Party Leader - Hastega/Protectga/Shellga

Unlike other buffing gambits this one allows you to control and make sure all your party members are actually hit by your ga buffs =P

Two more tips: if you have MP issues, either set yourself up with a Charge gambit (great way to restore MP if you're very low on it) or use Syphon on your attacking party members. They won't be needing their MP and if they're not in Shell it's a surefire way to drain all their MP to your mage in one turn. If they are in Shell status it may miss, so beware.