The mechanics for breeding are fine; the grinding for all the materials is what sucks.
When all you have is what you get from the story line you really only have enough to make 1 or 2 comps. After that you grind to be able to afford to catch breeders(or just buy them period), you grind to find the breeders, you grind to be able to afford braces, you grind for everstones or to be able to afford to buy everstones. You can pay to get a specific gender, you grind to be able to move set your pokemon(money for TMs, mushrooms, ect). It can take weeks to build a good team, especially for those of us who have real jobs and cant zombie in front of a computer for 15 hours a day.
Something I think might help is rebuffing payday, either make it to where we can use it more than 1 time per battle or make it pay out more per use. I understand that payday is meant to be the least effective way to make money, but it needs reworked. Its currently not even worth doing really. Sure its decent for things you buy at the marts or from NPC's, but the income you receive from payday doesnt hardly help at all when dealing with player to player transactions which is what makes the economy of the game. A rebuff could be a nice stimulus.