Powerful characters in themselves don't break stories, but Marvel has a bad habit of pumping characters way beyond what works. If Phoenix had stayed being just a powered up version of Jean, it would have worked better. Instead, they made it 12th on the list of the most powerful things to exist in the entire Marvel universe, Gods included. Superman is stronger than almost every Avenger, but his stories work because his opponents are a tangible threat, even when it isn't a world-ending threat like Darkseid or Brainiac.