For shadow Pokemon, I had a random thought. Would it make sense if you used HEX to edit a Pokemon so that it has extra evolutions? You could put the Shadow form of that Pokemon as an extra form, then have it evolve from that to its normal form by how much it loves you back. Also, you could have the shadow Pokemon as an extra in the evolutionary chain, so that if you had a Bulbasaur, it wouldn't need to be a Shadow Ivysaur first (like make Bulbasaur evolve into that by something random and usually unattainable, like Soul Dew or something, then Ivysaur, then Venusaur). And make objects that boost happiness incredibly rare.
Of course, however you go about this is up to you, and I'm interested in seeing how you work it out.