Boy, oh boy... Rayquaza. This guy is the definition of terrifying, and he's been that way since he was first introduced in 3rd gen. I remember how much of a pain it was to get to him; trying to run the Mach Bike over that crumbling floor... *shudders* And then there was the problem of actually catching this monster, especially since he was level 70 and you usually have Pokemon in their 40s-50s in R/S/E. But getting this guy is well worth the effort. Not only is his Attack a monstrous base 150, his Sp. Attack is equally terrifying at base 150. Base 95 Speed puts him behind a number of Ubers, but Extremespeed and Dragon Dance cancel out that downside. Base 90 defenses are a bit low for Ubers, but base 105 HP is nice. You might wonder how you can possibly defeat such a beast. The answer is...quite simple, actually. As a Dragon/Flying type, Rayquaza's Achilles' heel is his 4x weakness to Ice attacks. A decent Ice Beam can easily OHKO him, and since this attack is rampant in the Uber environment, it can be difficult for 'Quaza to find an opportunity to set up. If he does manage to set up, though, not much will be standing in your way to victory.
Recommended tier: Uber
Air Lock is Rayquaza's only ability, but it's invaluable in the weather-controlled Uber environment. As long as Rayquaza is out on the field, any weather effects are negated. That means teams revolving around Groudon, Kyogre, and Tyranitar won't be trolling you all day long. The fact that Kyogre is the most commonly used Uber makes this even more valuable.
Like most Ubers, Rayquaza has a vast and varied movepool. The newest addition to it is V-Create, a move that only Victini had access to before. This move has a whopping base 180 power, but lowers the user's Defense, Sp. Defense, and Speed by one level. Rayquaza can't get STAB and Sun boosts from V-Create like Victini, but it also isn't powered down by Rain, and Rayquaza has a far higher Attack stat than Victini. It best fits on a Choice set, where you'll want to be switching a lot anyways. Outrage is Rayquaza's strongest attack, but has the downside of causing Confusion. Dragon Claw is a safer, albeit less-powerful option. You can go with Dragon Pulse or Draco Meteor on a special or mixed Rayquaza.
Extremespeed is invaluable on any Rayquaza, as it helps him pick off faster, weaker opponents like Deoxys and Mewtwo. Dragon Dance and Swords Dance are two very useful boosting moves, though the choice between them can be difficult. Speaking of boosting, Rayquaza also gets Bulk Up and Hone Claws, but neither is as useful as the previous two. Ice Beam, Thunderbolt, and Flamethrower/Fire Blast are special attacks that provide a lot of coverage and filler on a special set. Overheat has a lot of power, but should only be used on a Choice or mixed set. The EdgeQuake combo is up for use. More fillers include Brick Break, Shadow Claw, Energy Ball, Waterfall/Aqua Tail, Earth Power, and Air Slash. Rayquaza even has a couple of support moves, including Toxic, Thunder Wave, Roar, Dragon Tail, and Tailwind. You should leave support to Rayquaza's teammates though; it doesn't have the survivability to pull it off.
Countering Rayquaza: As I said before, Ice attacks are Rayquaza's Achilles' heel. Nearly any decently powerful Ice attack will OHKO it. On the other hand, switching in is risky because Rayquaza can seriously hurt or even OHKO most of its counters as they switch in. Dialga is a reasonably safe choice, but Earthquakes will hurt it a lot. Lugia has great defenses as well, but Stone Edges are a problem. Groudon has enough physical bulk to stand up to physical Rayquaza, and he can OHKO with Stone Edge. Kyogre stands a chance if its bulky enough, and Scarfed variants can outrun and KO Rayquaza. Other Scarfed Pokemon (including your own Rayquaza) can revenge kill it, unless Dragon Dance is used. Extremespeed will also hurt a lot of would-be revenge killers. If you can withstand the assault, though, you have a pretty good chance of besting this Dragon.