Flygon has...
- Better HP, Attack, Special Attack, and Speed
- Fewer weaknesses
- More learnable HMs
Altaria has...
- Better Defense and Special Defense
- An earlier evolution
- Dragon Dance by level up
- Arguably a better movepool
Both these Pokemon are fine, but not great in Emerald. Both of them get their best STAB options from TMs, and Altaria has to rely on Aerial Ace or Fly for a Flying move. Flygon is generally considered the better choice thanks to typing and offenses, but if you're struggling with Grass types, I would recommend Altaria. Though there aren't many Grass types in the game, Altaria will usually do a much better job dealing with them than Flygon.
Altaria
Ability: Natural Cure
- Fly / Aerial Ace
- Ice Beam / Dragon Dance
- Return
- Earthquake / Dragon Dance
This moveset is physical, allowing you to take advantage of Dragon Dance if you so choose. Dragon STAB is unnecessary because the Dragon Claw TM detour isn't worth it and Drake can be moderately handled if you include Ice Beam on the set (though it will miss out on a few KOs). Besides that, Fly/Aerial Ace are your strongest STAB options, and Return/Earthquake hit whatever resists Flying moves.