I've been testing on PTGO Trevenant with Wally. If you go first, you can potentially get a turn 1 item lock with slows them down. I've also been trying to find a way to stop abilities. Silent Lab may help to stop Shaymin EX from using Setup.
Silent Lab is nice as it can block all the basic abilities that speed the deck up, Eggs, Shaymin, and perhaps Jirachi. The problem is this is a stadium against a deck that is stadium reliant.
I can see Aegislash EX slowing down Ray. The deck needs special energy to get quick attacks off. Sure, it can go the Mega Turbo route, but it will need the DCE eventually. The problem is Aegislash EX is too slow of an attacker but an effective ability none-the-less.
Aigeslash EX is a decent counter but from what I've seen it can go like thisGuys, come on, just use aegislash EX. I run it and despite never having tested against ray (because all my friends are too honourable to resort to a strategy like that) I almost always get an ideal setup turn 1. Plus, Aegislash EX is just the best thing against ray. Usable attack, high HP, and it beats most shredders 1-on-1, and if it doesn't just use Excadrill. Excadrill can even deal with safeguarders himself. Rayquaza's the most broken thing to have ever come out, but aegislash has what it takes to actually be a half-decent defensive deck in this format.
The only counter I can think of is luck. If you go first, start with Phantump and bench Shaymin EX. Draw cards and hopefully use Wally to evolve into Trevenant. Place Virbank as the Stadium and use Hypnotoxic Laser. Also, if you're lucky, you might also have an Enhanced Hammer and Xerosic. Use Xerosic and slap on a Head Ringer then play Enhanced Hammer.Aigeslash EX is a decent counter but from what I've seen it can go like this
M Rayquaza Player goes 1st, does the normal stuff
Opponent sends out Aigeslash EX on their turn, sends it active, attaches DCE, turn ends
M Rayquaza Player sends out Rayquaza EX and uses Intensifying Burn for 60.
Aigeslash then attacks with 99% chance of not OHKO'ing it
Rayquaza evolves into M Rayquaza, attaches energy, Mega Turbo and OHKO'S Aigeslash EX
Even with Ninetales, M Rayquaza can still KO Aigeslash because of how fast it can set up another one with no DCE and even a second one can't avenge KO it (yes with Bronzong it can but that requires you to have at least 2 Bronzongs out on the field).
M Rayquaza is like Siesmotoad, you think this counter is good against it but it doesn't work in the end due to it's Speed or Energy Denial
And how are Speedquaza players gonna burn through their deck? Well Ultra Ball, VS Seeker, etc and those are all items. And don't forget the Spirit Link.
Yeah and did you realize all but Shaymin are Items? Re-read my post and you'll know I was talking about using Trevenant+Wally. Check what Trevenant from XY base set does again .Simple. Shaymin, Ultra Ball, Trainer's Mail, Acro Bike, Computer Search, Juniper, Battle Compressor. I've seen my friends playtest a Speedquaza deck and managed to burn 1/3 of their deck rather easily in one turn.
Seismitoad might have a chance if using Quaking Punch, Lasers and all sorts of annoyances like Ringers, Hammers, etc.