1. For example, we take 2 pokemon that we want to sue to make an egg.
2. We then breed them in the genticaly enhanced breeding lab and get an egg.
3. Now that you have an egg, you hook it up to the DNA editor, this will tell you what pokemon will hatch from an egg and let you edit its IVs, ability, nature and egg moves.
4. Once finished we then let the machine speed incubate the egg to prepare it for hatching.
5. We now take the egg out and walk around for a few steps and have the pokemon you wanted.
This feature will only be available after you have completed the game (beated the E4 and champ).
This way it will make all the competitive people happy for a way to make "geneticaly engineered" pokemon. You ofcourse still have to level and train its EVs.
For EVs we have the training center, which will have a lesson to leave your pokemon to attend that trains a certain EV stat. You are able to leave at most 3 pokemon in each lesson. This takes time of course, but it would be a nice option for a freshly hatched pokemon and you can have multiple pokemon in the center while you go and do other things. Once again feature only available once the game is beaten.
So basically your suggesting a super easy way to get the values you want and not have useless pokemon, a requirement to do so, a way to prevent it from being too easy/ ruining the game, and on top of it all you clearly explained it...