Pretty much an expansion of what thutmose is saying.

When you have an egg, the following are put into play:
-1 IV is inhereted from the father
-1 IV is inhereted from the mother
-1 IV is randomly selected b/w the 2 again to be inhereted
-The nature is randomized, unless the mother is holding a Everstone; which it then gives it a
50% chance of passing the nature down (mothers-side).
-Egg moves from the father

This allows for one to actually breed better pokemon, by replacing the mother/father with a child who has better IVs, allowing for bigger chances for better bred pokemon. I'd like to see more tossed into inheretance; though what-i'm not sure. it just feels lacking (as a breeder, it does anyway).

Pokemon has a lot of inside stuff to appease to serious gamers, and not just kids/casuals.

http://www.youtube.com/watch?v=y57SRQ8YuIU

Perfect.

It would be kind of nice if they had some kind of breeding utility, rather than forcing breeders to look up move lists, stat charts, use calculators, and spend hours trying to figure out the proper breeding sequence and pokemon stats.

As it is now, the game doesn't give you any indication that there is more to breeding than just sticking two pokemon into daycare. That's likely why so few players have any idea about what actually goes on in the game's code when they breed.

I'm not saying that they should make it so simple that anyone and everyone has maxed-out pokemon, but they could certainly redesign it so that it doesn't take an eternity to get your desired results.

Maybe offer a limited number of "Breeder Licenses," which permit you to take advantage of special tools and allow those certified to breed pokemon commercially (think of the money they could make by selling licenses, and what they would earn by taking a cut of pokemon sales).

A breeding utility would be great - allowing you to look up IVs, EVs, see detailed information on stats, include calculators, breeding sequencers.

How great would it be to be able to set up a breeding sequence with conditionals and have the game automatically shift pokemon around to breed them in the desired sequence if/when/as certain conditions are met.

Rather then manually shifting pokemon in and out of daycare, you could tell the daycare lady to take a pokemon out when it reaches a certain level, or change pokemon when they've produced offspring with certain attributes, what have you.

I would like to have a breeding factory with an assembly-line. A system of breeding pens, incubators, computer programs, and automatic WiFi trading functions.

Sorry. I love complex systems - after all, I do design them for a living.