I still don't see a problem with one vs. two power sets, but I've stated as much in other threads. Others disagree. Nothing wrong with that.
While there are a great number of options and choices to make, this is still a dice game. Sometimes players are going to get lucky rolls...and if they have the PP, they can stack those good rolls to the heavens.
[On the other hand, I just made a roll in a Spatula's PBP game with 7 dice (3d10, 1d8, 2d6 & 1D4) and rolled 2, 1, 5, 6, 5, 2, 2. I'm just lucky I didn't have the Growing Dread limit! Sometimes the dice hate you.]
I just think that the game is meant to play fast (once you wrap your head around everything you can put in your dice pool and what you can do with your PP/opportunities...which I'm still trying to remember in actual play).
I think most of the other posters listed the best options to increase the challenge:
-Creative use of the Doom Pool.
-Creative Scene Distinction usage...set up a scene that plays against the common narrative usage for their abilities.
-Full use of all your tools including Assets, Stunts, Complications.
-Teamwork between villains...I.e. one setting up a Hero and boosting the next villain's chance to lay the smackdown.
-Split the Heroes up (or bring them together)...force them into group dynamics counter to their Affiliation strong suits.
-Take note of hero limits.
Just some ideas and some that have already been mentioned, I'm sure.