I would begin by breeding a couple of 5IV and 6IV Pokémon with egg moves the normal way, and sell these to rich trainers.
After I have accumulated enough capital, I buy up the daycare (or found one myself), and expand it. I hire breeders and IV raters to breed penta-/hexaperfect Pokémon, and pay trainers to catch me the Pokémon I need, and to train males to a certain level where they learn a move I want as an egg move.
Pokémon with less than 5 perfect IVs, or with bad natures, I keep in the daycare until they are level 5 or so, and then release them into the wild. If they are a foreign species and would disturb the ecosystem, I instead ship them to third world countries and sell them at low prices there.
Any penta- and hexaperfects I sell to trainers and collectors at high prices, and shinies at a premium.
The next step, once I can afford the massive investment, is to buy up land and grow berries in large quantities. I open stores across larger cities in the region where I sell berry juices and Pokéblocks – and to create a market for the latter, I open a couple of contest halls in the region and host Pokémon Contests. Though this scheme costs quite a lot, it could pay itself off very quickly: entrance fees, ticket sales, ad revenues/royalties from broadcasting the contest, and demand for my Pokéblocks.
Once my conglomerate of breeding centres, berry farms, and contest halls has enough economic clout (at this point I would probably call it Team [something]), I lobby the regional government to introduce certificates for Pokémon caught or bred in the region (like the pentagram of Kalos) to prevent competition from genners and other regions. I also start exporting the Pokémon, since the regional market would eventually be saturated.
At this point, I'm probably making money like a Persian holding a Coin Amulet. If my business runs smoothly, I take a few pentaperfects from my daycares, and go on a new adventure with them (incognito).
