Well, here's what I've been doing:
- Get a female with the right Nature and a few perfect IVs. Usually I'll take her from a Friend Safari to ensure at least two perfect IVs and use a properly-Natured Ditto (preferably Friend Safari Ditto) or compatible male with an Everstone, which passes down Nature, to hatch a female with the correct Nature. Once I have a female with the right Nature and a couple perfect IVs, I give her the Everstone and put her in the Daycare.
- Get a male with a couple perfect IVs. Again, probably from Friend Safari, or maybe just a reject from a different breeding project who happens to be a species that can mate with the female (when I started breeding Minccinos I was at an advantage because I already had 5IV Mawiles and so I was starting off with a high-quality male). Make sure the perfect ones are in different stats, for instance a female with perfect HP/SpD and a male with perfect Att/Spe. Give the male the Destiny Knot and stick him in the Daycare.
- Okay, so now you've got two pokemon in the Daycare with two perfect IVs each. Start hatching eggs. The Everstone will make sure that the offspring have the correct Nature and the Destiny Knot will pass down 5 IVs at random from the twelve provided by the parents (for example, it might choose the mother's HP, SpA, and SpD and the father's Att and Def). Hatch until you get a pokemon with 3 perfect IVs (or even 4... lucky you!). Replace the appropriate Daycare parent with the superior offspring and keep hatching (make sure you give the offspring the item the parent was holding!). Now you might have a female with perfect HP/SpD/Spe and a male with perfect Att/Spe. This will slowly ratchet up the quality of the parents until you have two parents with 4 perfect IVs each, giving you a bunch of awesome babies.
- Ah, but we only started with 4 perfect IVs in our pool: HP/Att/SpD/Spe. How do we work in Def or SpA? What I do is wait until I have, say, a female who has all 4 of the perfects we started with (so a 31/31/xx/xx/31/31 female) and then replace our male with one that has perfect Def or SpA (again, probably from the Friend Safari). This will temporarily lower the quality of babies since this male probably has fewer perfect IVs than the male he's replacing, but he's introducing 31s in stats that didn't previously have 31s, so you can ratchet up the quality as before. Rinse and repeat.
OTHER TIPS:
- Save a lot of the 4IV and 5IV offspring, even if they're in stats that aren't ideal (like if I had a Mawile where the imperfect stat was Def when I would prefer it to be SpA). 5IV and 4IV pokemon make great trade fodder so that when you start up other breeding projects you can start with a lot of good IVs because you traded one of your extras to somebody.
- Don't just release all of your 1IV/2IV/3IV rejects. Instead, Wonder Trade all of them. You'll rack up a TON of miles which you can exchange for items (Heart Scales, PP Ups, Moomoo Milk... I hear you can even buy a Master Ball for 7500 miles once you've unlocked it)(I think you unlock things in the PokeMile store by earning more and more medals).
- You can check your IVs by talking to the guy in the pokemon center in Kiloude City. The things he says are kind of vague but you're looking for the "stats like that can't be beat!" line. If he says "Incidentally, your pokemon's greatest potential is its HP, Attack, Defense, and Speed!" it means you have perfect 31s in HP/Att/Def/Spe.
- After you check with the IV guy, go to your pokemon's summary screen and mark the perfect IVs. Do you see those six symbols (heart, star, circle, square, etc.)? Pretend they represent HP/Att/Def/SpA/SpD/Spe, in that order. You can just tap on the symbol to fill it in. This will help you keep track of which pokemon have 31s, how many they have, and in what stat.
- Don't worry about getting a 6IV pokemon; it takes a long time and is pretty pointless in almost all cases. Mawile doesn't need its SpA and so I just shoot for 31/31/31/xx/31/31. If it has an imperfection in something other than SpA (say, a 31/31/xx/31/31/31 individual), it still makes great trade fodder because, hell, it has 5 perfect IVs. Don't use the GTS, though. Go to a forum (I prefer SomethingAwful) that has a good thread with a lot of people breeding a lot of different things. You can get some pretty cool stuff for your cast-offs.
- If you use Super Training for your EV needs, a good time to hit the punching bag is while you're biking back and forth hatching eggs.
edit:
- If you want a Hidden Ability, you're going to want to start with a female who has that ability. As you replace Daycare parents with higher quality offspring, make sure you never replace the female with one that doesn't have the Hidden Ability, assuming the HA is what you want the final product to have.
- Egg moves! I usually put these on first. When I wanted Rock Blast Shellders, I bred a male Armaldo with a female Skill Link Shellder until I had female Skill Link Shellder with Rock Blast. Then I bred with a Jolly Ditto so that I would have a female Jolly Skill Link Shellder with Rock Blast. Then I started using male Cloysters and Shellders to ratchet up the IVs.
