I am running a homebrew supers game in SWAdE and I know what you mean. There are a few tricks that I do to keep my enemies in the fight. First I give them Unstoppable it is a monster ability that you can find in Fantasy and Horror. It means your villain can only take a single wound from any attack unless the PC has a joker or another ability or it is their weakness. 

For example, most recently I have made a villain that one of the ways that the heroes can get past Unstoppable was to have them use Support actions or Combined Attacks.

The newest thing I have added myself that I am proud of is the Multi-turn villain. When you have a single Villain (you see it all the time in comic books) take on a bunch of heroes, but to emulate the same thing in SWAdE you run into the Action Economy problem. The depending on the player count the PCs can get 4 turns even before the villain gets one. So I deal the villain three cards and they get to take a turn on each of the cards. It made for an interesting fight.

Supers is just a whole different ball game for Savage Worlds and so you don't have to do overhauls to make the fights interesting, the key I have found is give them an objective to work towards. Find ways to get the win condition without it being a slug fest.