The missions of absoul and tyranitar, I can not do them because I am missing 4 ivs and 2 ivs, I do not know how many the same happens to them, but should they remove that requirement?, I don't see much case that they are exactly 22 and 120 ivs.
Well themed Pokeballs do not think they would lose their value, since they have their use apart from appearance. But I still think that an npc that helps you change the pokeball of your old Pokemons would be good, since they have the basic pokeball despite being caught with masterball or ultra.
how about having an npc. that in exchange for money you change the appearance of pokeball. it would even be interesting to have unique appearances with the pvp and pve seller.