Gym leaders - Standard not much changed.
Gang Admins - While not taken directly out of the games. I feel as if it would be interesting to have these as middle men between small hideouts and the base. Hide outs could have their location be given by completing quests. When an admin is beaten it gives a part of a key to the Base. Beat three admins of the same team you get the team's evil base. To separate the teams each team would be divided by biome. (Rocket in plains, Magma in deserts, Aqua in swamps, Galactic in mountains, Plasma in forests, Flare in the nether, and the Aether foundation in taigas)
Gang leaders - the final boss at the end of larger base dungeons.
Elite 4 /Champion - self explanatory
Other boss types could be included but I feel as if these and new boss pokemon (Gigantamax and totem mon) would fill out more incentives to explore and battle.