I didn't find the Black Spindle/NttE quests challenging in the slightest. Raid mechanics are challenging. The mechanics in the exotic missions were annoying and stupid. Throwing 80 enemies into a tiny room with a time limit is the opposite of difficult to me. Bungie doesn't know how to do difficult.
I find the Black Spindle mission's design to be one of the most subtle and clever in the whole game.
The time limit is there to make you rush to the boss, and then be conditioned to try and focus him to kill him asap, which is exactly what will usually lead you to your doom because it will generate way more adds than you can handle.
I loved having this epiphany after several wipes that you have to methodically clear out the balls, then the adds, then shoot on the boss to trigger the next wave of balls/adds.
I much prefer this mission (or the paradox one) to KF, because it's "organic": there's not only ONE way of doing this encounter (just one easier way than some others), and you can improvise and play several roles if you want to. KF, in comparison, is just so mechanically stiff it's boring me to hell...