How do you run a game where the characters exist outside of time and space?
How do you reflect abilities when reality itself is malleable?
Is it possible to simulate difficulties for tasks when reality can be bent to your whim?
The RPG Amber dealt with things like this quite simply, Mage: the Ascension did some work in a similar area.
Perhaps the easiest way to deal with variance between characters in this sort of setting is to give them spheres of influence. Are you a god of thunder? Does manipulation of the weather provide an advantage in this situation? If so, and you can suitably justify it, gain a bonus. If not, sorry, try something else.
The problem with this notion is players who come up with generic "specialties" that magically become useful in every possible situation. So maybe we need to implement an idea that says "the more you use a specialty, the harder it is to keep using it". Use it once, standard difficulty...use it twice, difficulty goes up by 1...use it again, and difficulty goes up by 2...this continues until it just becomes unfeasible to keep exploiting this aspect of reality bending. The penalties might start to decrease again as a character starts using the other powers at their disposal. But then you might get a character who ends up as a two-trick pony, simply alternating between their "incredibly lucky" and "irrepressible" advantages which both find easy application in almost any activity.
Maybe it would be fun to allow every player to pick a power/advantage for themselves and a power/advantage for someone else. This would allow them to gain a bit of control over what they want to play, while throwing in a random element.
Maybe each power is linked to a specific type of activity...opening options in the timeline, transforming destiny, and collapsing quantum waves into specific events. Creation, Transformation, Destruction...maybe I've still got Walkabout sitting in the back of my head.
I'm starting to lose a bit of focus in the ideas for this game. Time to start tying things back into the core ideas again.