Changes in Generation 6
Egg Moves - In past generations a Pokémon could learn special moves that it normally does not learn by inheriting it from the father only. In X&Y this has been changed. Pokémon will be able to inherit these Egg Moves from the mother as well. This opens up new possibilities for move combinations that could not be obtained before.
Hidden Abilities - Previously referred to as Dream World abilities, these abilities are not normally obtainable by a Pokémon. These Hidden Abilities can be found on special event Pokémon and sometimes on Pokémon in the Friend Safari or in hordes. These abilities previously could only be passed down by female Pokémon but that has been changed in Generation 6. Male Pokémon are now capable of passing down Hidden Abilities while breeding with Ditto, but have a smaller chance to pass them down than a female. Female Pokémon have a greater chance of passing down the ability. Breeding a male Pokémon and a female Pokémon with a Hidden Ability yields the best chance to pass it down.
Special Poke Balls - Arguably the most important change in breeding is the passing down of Poke Balls. In all previous generations, Pokémon that were bred would always appear in normal Poke Balls. In Generation 6, the baby will inherit the Poke Ball from its female parent (Note: Ditto does not count as a female). Rejoice in fact that your bred Pokémon can now be super stylish!
Things Required for Breeding Strong Pokémon:
Friend Safari - This is the starting point for getting Pokémon with perfect IVs. Every Pokémon caught in the Friend Safari is guaranteed to have at least 2 stats with 31 IVs. In order to start breeding, you need to find Pokémon in the Friend Safari that can breed with the Pokémon you are looking to make. Catch some Male parents from the same egg group as the Pokémon you are breeding with different 31 IVs to pass down to your baby, grab a female of the species you want with the ability you want to pass down, or if you're lucky enough to be able to find them in your Safari, catch some Dittos so you can pass down IVs to anything.
Synchronizers - Pokémon with the ability Synchronize are extremely useful for getting the Natures that you want. If a Pokémon with Synchronize is the first Pokémon in your party (fainted or not), there is a higher chance of the opposing wild Pokémon having the same Nature. This allows you to catch parents with the aforementioned 2 31 IVs and with the right Nature to pass down to your offspring.
Everstone (Geosange Town) - Everstone is important for maintaining the Nature of the Pokémon you are trying to breed. The parent holding the Everstone is guaranteed to pass down its Nature 100% of the time.
Destiny Knot (Cyllage City Hotel) - Destiny Knot is the most important item for breeding perfect Pokémon. Without Destiny Knot, offspring are limited to inheriting a maximum of 3 IVs from both of its parents. In Generation 6, Destiny Knot raises the limit to 5, allowing a Pokémon to inherit almost all of its IVs from its parents.
Power Items (Battle Maison) - While the Power Items (Weight, Bracer, Belt, Lens, Band, Anklet) are not necessary, they are useful items to have for the early stages of breeding. Attaching a Power Item to a parent guarantees that it will pass down the IV it has in that specific stat to the offspring. This is useful for preserving harder to get IVs such as a 0 in Speed for a Trick Room Pokémon.
IV Judge (Kiloude City Pokémon Center) - The IV Judge will take a look at your Pokémon and tell you what stats they have 31 IVs in. If the judge says X stat can simply not be beat, then congratulations, you have a fully maxed out IV. On the flip side, if the judge makes a comment about how terrible the IV is, then congratulations, you have a 0 IV in that stat!
Flame Body - While a Pokémon with Flame Body is not required, it is extremely helpful for speeding up the process of hatching eggs. Carrying a Pokémon with Flame Body in your party allows you to hatch your eggs in half the time!
Note: These steps do not have to be followed in an exact order. This is merely a guideline to help you get into the process. You can do things in almost any order, but this is the most streamlined approach.
1. Grab a Pokémon with Synchronize and hit up the Friend Safari! Your goal here is to grab a bunch of parents for the Pokémon you are trying to breed. You will want as many males as possible with different combinations of the perfect IVs to pass down to your offspring as possible. Leading with a Synchronizer will help ensure that you will have the Nature you want in your arsenal to pass down.
2. Attach an Everstone to the parent with the Nature that you want to pass down. Breed that parent with a female of the Pokémon that you are looking to get. Hatch the eggs until you have a female with the Nature that you want. Move the Everstone to the baby. From this point on, the female will continue to hold the Everstone to continuously pass down the Nature.
3. Breed down 1 or 2 IVs from a male parent. You can do this a number of different ways. If you have a male parent with 3 or 4 perfect IVs then it is probably better to attach a Destiny Knot to it to allow it to pass down as many as it can. If you are not lucky enough to have that many perfect IVs yet, you can attach the Power Item that corresponds to the the IV that you want to pass down to the father to force it to pass the IV to the baby. For example, you have a Ditto with 31 HP and 31 Speed. If you attached a Speed Anklet to the Ditto, the offspring would be guaranteed to have 31 Speed.
4. After obtaining a female Pokémon with 1 or 2 perfect IVs from the father, you can replace the female that is currently in the daycare and move the Everstone over to the female. Pick a male with 2 perfect IVs that are different from the female and attach a Destiny Knot to it. This allows for more IVs to pass down to the baby. The goal here is to keep improving the number of perfect IVs on your female.
5. Once you get 3 Perfect IVs, switch the parents again. The female with 3 IVs replaces the female with 2 IVs and a male with another combination of IVs that are not perfect on the female replaces the male. Remember to keep Destiny Knot and Everstone on the respective Pokémon so that IVs and natures continue to pass. Your goal is to end up with at least one 31 in each IV you want to pass down between the parents and as many 31s in important stats between the parents as possible to maximize the odds of your Pokémon inheriting 31 IVs.
6. Rinse and repeat until your Pokémon are powerful. Keep in mind that as you build up your collection of Pokémon, this process gets simpler. Males with a large number of perfect IVs can be used within their Egg group to speed up the beginning processes of breeding. The more perfect IVs between the parents, means a larger chance of getting what you are aiming for.
With a little bit of luck you'll have your perfect Pokémon in no time!
If you have any questions, feel free to ask us in the Breeding Q&A Thread.
Good luck and happy breeding!