Before I go on, its worth noting that the Pokemon in the Egg will always be from the line the mother is on. So if you have a female Buizel in the Day Care for breeding, you will get a Buizel from the Egg. The only exception to this being when breeding with Ditto; the Pokemon hatched will always be that of the father or mother, depending on which one is not a Ditto.
The effects of breeding are really only visible most likely in Egg Moves. There are some moves that certain Pokemon can only learn via breeding with other Pokemon, such as Sneasel with Pursuit and Eevee with Wish. Since the Pokemon the Egg will hatch into is determined by the felame Pokemon, the male Pokemon is the one that must have the Egg Moves you wish the hatched Pokemon to learn. There is actually also a trick you can use with the Everstone that allows you to 'manipulate' what nature the hatched Pokemon will have.
In essence, breeding is probably something you don't really have to worry about, unless you're planning on playing the game competitively or just wish to have a particular move on a particular Pokemon.
Forgot about Baby Pokemon, lol... ^^;;
Hope that was of some help... ^^;;
