The most problematic powers are the ones that are most asymmetric. Super-Alice can affect Super-Bob, but Bob can't do the same. Alice can read his mind (Bob's powers don't include mind shields, which are normally reserved for psychic powers), or teleport him into the upper atmosphere (Bob can't fly), or use her ESP or astral projection to find his secrets (Bob can't block ESP, and isn't even aware of it).
There are several ways to handle this general problem.
- Alice's powers are effective, but Bob has some other power that can be used to counter them. For example, Bob has regeneration and self-inflicts pain to block someone from affecting his mind. Or Alice has speedster powers, but Bob can project a fire aura around his body that Alice can't punch through without hurting herself.
- Alice's powers are effective, but one of Bob's teammates can assist him. For example, Bob can't fly, but a successful Defend action means that a flying teammate rescued him in time. The flying teammate might also be the character rolling the Defend action, using her own power facts to justify doing so.
- Alice's powers are effective, but something unexpected or interesting happens that drives the story in some direction other than "Alice wins". For example, Alice's ESP might reveal that Bob rescued Alice's kid sister from a disaster and is paying for her hospital stay.
Many of these options are mechanically handled through Create Advantage or Overcome mechanics. If or when a roll is appropriate, "failure" doesn't have to mean "Bob successfully blocked the attempt", only that "what Alice wanted doesn't happen the way she wanted, or happens with complications", and success doesn't have to mean "Bob loses".