For example, in the Nether, we could have a Pokemon like Rare Turtonator Bosses spawn that would shoot projectiles similar to Blazes. These projectiles could be explained as being a Will-o-Wisp move. Turtonator is a Pokemon of which it would make sense for it to shoot projectiles out of its mouth. They would also sometimes charge at the player and force a battle, similar to Ultra Space Pokemon. They would have the same spawn behavior as Blazes, and would stop spawning once their respective spawner has been broken. They would drop loot that is unique compared to other Boss Pokemon, giving more of a reason to come to the nether in the first place.
I imagine these bosses wouldn't have a different color like boss Pokemon do currently, they would be their normal color while still being boss Pokemon.