Here are some good IN-GAME moves to teach your rayquaza:
I would use Dragon Claw because of its moderately high attack power
(80 I Think) and because its got a relatively decent amount of pp. Great for taking out the elite 4. Rayquaza gets this attack at level 20 or you can get it in TM 02.
Ice Beam Is not a horrible move either it has 95 power, good accuracy and it can cause freeze. It is great for lorelies pokemon (first member of elite 4) It will plow through her water pokemon especially if your rayquaza is EV trained correctly (TM 13)
Thunderbolt Is a good choice for the RPG as well. Its high attack power and accuracy are also good for tackling the elite 4. Also it has 15 PP which is pretty good for a powerful move like that. <-- Definitely Reccomended (TM 24)
Flamethrower would be great for the final slot. It covers yet another element and combined with the other moves i reccomended can wreak havoc on many of the games teams. They all cover a ride range of weaknesses and have high attack and accuracy stats which is good.
If you want to (depending how much your pokemon likes you or dislikes you) you could use return or frustration, both decently powerful moves.
Another good choice would be earth quake. Perfect for double battles when your partner is a flying pokemon. It will hit both the enemy pokemon but your partner will take no damage. Also it has 100 power which is high.
Post the rest of your teams as well with their attacks.
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