If you must choose to power up only one Rayquaza...

Double dragon.
For machamp raid, I can use Mew2 instead.

I am powering a dragon but will probably be looking to power a flying as well

In the long run I will want the flying. You can fill in your dragon roster with maxed out dragonites/sallys while for your flying roster there is...only rayquaza who is competitive

I have two +90IV, one with air type and the other with dragon. I powered up the former reason being it is useful in Machamp raids. Although there are other options, I like to try out different attackers than using Lugia all the time.

If I had to pick one, flying, since I already have a maxed 100% DT/O Dragonite.

Double dragon for now. Although I have 2 maxed drags, Ray is a DPS upgrade and will be best TTW vs Latios and Latias.

Flying doesn’t have as much use except machamp.

I just finishes maxing one and it is double-dragon right now vs Rayquaza raids and has already served me well the past week in that slot. There will be other dragon type raids also in the future. Have not raided one Machamp in about half a year at least? Don't plan to do so either. So don't really see the point for me there.

Also there isn't exactly a TM shortage, so if there will appear some super bug/grass raid in the future.... it's always changeable. (I never power up by moveset (unless really good legacy) but by IV)

Double dragon for now, useful against itself, both of the Latis and Palkia in the next gen. Later on I may TM it to double flying.

My first Rayquaza is a wonder with double-flying moves. With less free time to raid, I will probably stick with that one. Already have four wonder Dragonites with DT/OR, DT/Hu, DT/DP and SW/HB (planning to TM eventually); hoping to get one with DT/DM during the Community Day.

I will only power up one with dragon moves. I consider that the current flying moves are too weak to be bothered.

I set out to get a double-flying Ray today and I got him. I'm actually more excited about this one than the double-dragon one because I've got 2 good Dragonites. I only wish I could drop him in a gym

Double dragon for sure. I already got moltres for grass and bug. For fighting types, Rayquaza performs similar to Espeon. Dragon specialist will fare well in lati raids as well. Generalist position is just a bonus for me.