Honchkrow is better than Rayquaza DPSwise, so I don't think it'd be a good idea to make flying type Rays.
And as you know you're also losing top DPS dragons. Latios is duoable with 6 35lv Rays for each account in windy/best friends. I'm bit lazy to calculate about the case of 3 maxed Rays and 3 Dragonites, but I think it has potential.
Consider TMing Rayquaza to flying
With the dawn of Dialga/Palkia, and catching good ones of both, I am potentially looking at more additions to my team of 12 maxed dragons (3x rayquaza, 7x dragonite, 1x salamence, 1x latios) which I clearly do not need. Begs the question- should I TM the Rayquazas to flying moves?
Pros:
1. Flying type is covered and I can transfer some filler flying pokemon like underlevelled Lugia, Rayquaza, staraptor, honchkrow etc to free up bag space
2. Rayquaza is a much better flying type than if I were to substitue it with a hurricane dragonite, sky attack lugia or similar
Cons:
1. Obviously I lose out my best 3 dragon offense. It will be a hard hit to swallow but I have Dialga/Palkia to back it up. Running 3 rayquaza is not exactly like the setup needed to duo Palkia/Latias anyway- for those challenges I need to be running 12+ maxed rayquaza with another player.
2. Dragon ascent is a flying type. Come the day Ray knows its signature move and it's not TMable, I might wish I had stuck with the dragon set instead.
Let me know what you guys think.
Answers
Personally, I would keep the dragon moves on Rayquaza for the following reasons:
1. Although we have several new dragon-type Mons to add to our lineups, none of them dethrones Rayquaza as the king of dragon DPS.
2. How often do you find yourself in need of a flying-type specialist? Imo, its a fairly limited niche. Ray is likely better served with dragon moves where it functions as the top dragon specialist and also a top-tier generalist (if anyone still uses those).
We know the Salamence has DracoMeteor, plus whatever Palkia/Dialga you might power up. How many of those Dragonite have Outrage? Maybe consider trading one of the Rayquaza for something you consider valuable...I traded a max Dragonite to my B account. I have many, many, many lucky Dratini. Yeah, turned out terrible though, 3762 went to 3566, whoops. It was pretty old, too--first half of 2017.