Which would you power up?

Neither. But out of those two, definitely not Rayquaza nor Mewtwo.

IV wise your Rayquaza is plain awesome and very useful (though expensive). Depending on your Dragonite situation, it might be useful for you.

So wait for a better Mewtwo is my advice.

Powering a perfect RQ will help you with other RQs...My wife got a 98 and a 96 with 15a already both OR, putting dust candies into those already (she has only 1 Dragonite and 3 Mewtwo at level 30). Personally, none of the 4 RQ I already have are over 2030...then again, I have 4 Dragonites powered near or above 3300. EX invites are being thrown quickly right now...was just at one with over 60 raiders there

Neither, you should transfer both the Mew2 and Rayquaza to the professor to get the extra candy

Which do you need more, a Mewtwo with (moveset) or a Rayquaza with (moveset). Power that one up. You'll eventually power Rayray up, but for now, power up what you need, and start doing more Rayquaza raids. That way you'll get rare candy, and Rayquaza candy when you catch him, even if he's a 10/10/10.