What about if one of the decks was like a ‘sidekick’ deck?
This would require a rules addition, with Sidekicks being optional. Sidekicks would be Heroes with their own character card, but would be associated with a main Hero, and all their cards would play in the hero’s play area. Sidekicks wouldn’t have a power, however. Instead, they would have a ‘Support’ keyword (similar to The Operative’s ‘Command’ keyword). Then the main Hero would need to use their ‘& Sidekick’ variant, whose power would be to use the ‘Support’ effect of their Sidekick. This ‘Support’ effect would be to play the top card of the Sidekick side deck, or something similar.
Sidekicks are useful, often times providing a helping hand at a critical moment, or foiling the main villains plan in the background while the Hero is going toe to toe with them in the foreground. But sidekicks also get into trouble, often requiring the Hero to take time and effort to rescue them. The Sidekick deck could have useful one shots as well as ongoing cards that help the Hero out, but also some that cause complications for the hero. The tradeoff is giving up the Power of the Hero (which usually helps them build their engine) in exchange for the Support of the Sidekick, which could be more powerful or possibly a hindrance.
In addition, if the Sidekick counts as a Character card, it can also be Incapacitated. All the cards from the deck would go away, but it would still have a Support effect on it’s incapacitated side that would be something smaller, but still helpful, much like with Heroes.
This could also work with a dual Hero situation, where one is the main Hero, but can call on their companion as their ‘Power’, who has their own separate deck with its own effects. However, with the Sidekick mechanic, multiple characters could have a ‘Sidekick Variant’ allowing them to play with any Sidekick.