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Okay, so here's my idea to get Gen III mons into Gen VI with just one system: first off, release FRLG and HGSS on the eShop. Second, release an app that will allow you to connect Pokemon games together, and I'll explain this in a bit. For example's sake, let's call it Pokemon Link.
In that app, you can choose one of the Nintendo DS games and have it link to another game so that it'll be ready for Pokemon transferring. Again for example's sake, I'm just going to mention Pokemon Black 2, Heart Gold, and Fire Red.
You catch a Pokemon in FireRed, give it some unique Gen III Tutor moves and then beat the game or do what you need to do to get ready to transfer it over to Gen IV, Heart Gold. Then, you play HeartGold far enough to access Pal Park. Once both games are ready, you go to the Pokemon Link app and first select Heart Gold, and link it to FireRed. When you now play Heart Gold, it'll act like FireRed is in the slot, allowing you to transfer over Pokemon from it via Pal Park. And if desired, I believe there are places where the inserted GBA slot will affect what kind of Pokemon you encounter.
Next, you want to transfer that Pokemon to Gen V. Since HG and FR are downloaded, you'd have B2 as the retail cart put in the game slot. Progress far enough in Black 2 to use the Poke Transfer, and then go to the Pokemon Link app. This time, link Black 2 to HeartGold, and unfortunately I can't remember how the process works exactly, it was something involving DS Download Play and requiring two systems or whatever. But that's not what we're going for. In this case, in the Pokemon Link app, once you link Black 2 to HeartGold, you can select six eligible Pokemon to transfer over, so no Pokemon with HM moves. Once the six have been registered, go back to Black 2 and go to the Poke Transfer and do the process like normal, and then once you save and successfully get them, that'll also save the Heart Gold data so that the Pokemon would transfer over and are gone from that game.
