Challenges get disproportionately difficult as it goes on, even with the increase in power with the Pokemon. You also start facing more bosses and gauntlets with evolved mons, so it stops being a game of "kill the mooks and move on". It's even worse farther down when challenges were made with +++ or ++++ trait Pokemon in mind, which were cut super late in development.
There's 100 minions per boss iirc. Killing them all nets you good cash, you'll recruit a bunch of those mons, and it makes wobbling the boss easier. The exception to this are transforming Pokemon, like Aegislash and Meloetta. I believe it's a bug in which the game just thinks you've beaten the boss and stops spawning the minions.