EV is effort values, not the happiness rating. Every 4 point of EV means +1 stats to a category. Each Pokemon can get up to 512 EV (or is it 510? *shrug*) so by manipulating EV you get a great amount of boosts in EV. EV comes depending on what Pokemon you fight against, such as a Zigzagoon gives you +1 EV Speed so if you want to be fast, you'll want to battle lots of Zigzagoon. Each category can consume up to 252 points of EV, so you can boost a stats up by a bonus of 60+ points worth of stats. If you having a Rayquaza, and you're fighting against another one, knowing how to play well with EV will give you a 40 stat boost (equilvalent to 10 lvls worth of stats roughly). So in a short summary, know how to play your EV values and you will be at lvl 110.
Since the above talks of getting EV to boost your stats, this should be easier to understand. Since there's a maximum of 510 EV only, you can't afford to have every stats getting the EV Buff. You can't afford both special attack and attack to be boosted at once (or else you'll be a defense-less slow Pokemon that'll get KO before your heavy attack power can strike). So that's why we discourage both dragon claw and fly at once, as one uses special attack stats, while the other uses physical attack. EV boost can only boost one of them, so one of the attack will be pathetic attack power. So let's be more efficient by either using only special attack or only physical attack.
Now, it's time to analyze EVERY SINGLE move you have on your team, and why an attack isn't worthwhile on it.
Blaze Kick- well a fire attack with just 90% accuracy and 85 power is trash... why not flamethrower with 95 power, 100% accuracy and 5 more PP as well? It's just wasteful to rely on the 25% critical hit when most likely all opponents will be dead in 1~3 flamethrowers (so by the time you got a critical hit, flamethrower already KOed). Plus accuracy factor... so at least replace blaze kick with flamethrower
Sky Uppercut- 85 power, 90% accuracy again with 15 pp... brick break has 75 attack power, 100% accuracy with the same PP, but has a nice side effect of destroying reflect and light screen. If there's reflect in play, I'll love to see what can Sky Uppercut do. If you say that "Sky Uppercut hits fly though!" Well... why don't we analyze fly?
Fly- 70 power and 95% accuracy... takes a turn to fly (dodge an attack) and then attack. So this is a 2 turn move, right? Well... 70/2 = 35. You're pretty much using a gust, and it's not even as accurate as gust. It's not like it's PP is that attractive either. But what about the dodging factor? Well... this will happen
Rayquaza flies high
Milotic ice beam misses.
Opponent thinks: "oh... he's going to hit me with fly next turn... let's...
Opponent withdraws Milotic and sends out Aggron
Rayquaza uses fly
*does 10 damage to Aggron*
(insert Opponent's evil laugher and harsh comments here)
So much for your block. You gave the enemy a chance to switch in and out safely. If you used aerial ace for example, you could have attacked that Milotic and deal more damage (but in reality, if you're Rayquaza and you see a Milotic, you either run or try to KO it as you know that you won't live ice beam)
Fly is only used when you're trying to stall... toxic users like Crobat will actually want to use fly because all they want is to stall a turn, not the damage factor. Rayquaza is trying to sweep, not to give the enemy a chance for leftovers to heal up. Plus if the opponent are resting and you used fly... well well 1 free turn for the enemy to wake up from Rest...
Doom Desire- exactly what can this move do? 85% accuracy with 120 attack power... However this thing has no STAB as it's type is neutral ("struggle type"), and just darn poor accuracy. Plus you have to wait for a few turns for it to kick in. Why don't we just use psychic to knock out the opponent now instead of waiting around for a few turns suffering attacks from the opponent? Best offense is best defense. This attack is pure trash. (but then again, Jirachi just suck period)
Eruption- a powerful attack that has diminishing outcome as your hp goes down... but excuse me what's Groudon's speed? You're quite likely to gurantee to suffer one attack before you strike (assuming that your opponents are half decent). So really in reality, you are using something slightly more powerful than fire blast the first turn, and then something weaker than flamethrower the second time you use it. Not to mention, Groudon's physical attack power is base stat 150, while special attack is just base 100. Eruption doesn't even get STAB... why bother...? You're not Kyogre with the STAB+150 Sp.Attack+rain dance boost all at once... you're just Groudon. (plus even Kyogre using Water Spout requires setting up for bonus speed)
Hyperbeam- absolute trash attack (unless on Slaking)... so 150 attack power with 90% accuracy... sounds good? However the next turn is gurantee to miss a turn... so it's a 2 turn move technically. 150/2 > 102 from return... doesn't look so good anymore hmm? Just use 2 return continously, and your attack power overcomes hyperbeam. Not to mention, if the opponent survived that turn of hyperbeam, they get a free turn to do whatever... they can recover, use dragon dance to sweep, or a free turn of focus punch... blah!
Swift- ok... Return has 102 attack power (42 higher than swift), and has 100% accuracy. In this case, accuracy doesn't even matter unless the opponent uses sand veil, double team or brightpowder... However if you hit them fast enough, they won't have the endurability to use 6 double team. So Swift is useless as well (and shockwave). Aerial Ace would have been useless as well but unfortunately we have no other better flying attack (however there's return for normal, and thunderbolt for electric)
And just how deadly is calm mind, dragon dance and other buff up...? Let's use your Rayquaza for a demonstration of dragon dance's wrath. Assuming lvl 100, with 252 EV in Attack power, 252 EV in speed, with the adamant nature to give attack power x1.1 boost and dropping special attack by 10%. You get this stats so far...
352 hp, 438 attack, 216 defense, 289 speed, 302 sp.attack, 216 sp.def
What happens if you use one dragon dance...? it boosts attack and speed, making it...
511 attack and 337 speed... it's quite a difference. The attack boost is simply too amazing that now you can knock anything out of your path in one attack. You don't have to use all 6 dragon dance. Just use dragon dance once or twice and it's close to a gurantee you'll be taking down at least 2 of your oppoennt's pokemon. If you're not afraid of a Rayquaza getting a 73 point attack bonus in just one dragon dance (not to mention speed), I don't know what you're afraid of...
Hope that helps clarifiying things a bit. If you still disagree, say why and we'll continue on talking about this.