You know what's always cool about superhero origin stories?

The transformation of the protagonist.
That's what Joseph Campbell's "Hero with a Thousand Faces" is really about.
That's what the first 3/4ths of the novel "Jumper" (by Steve Gould) is about.

In my personal holodeck (ie: my imagination), I bet that a well-tuned IIEE design can accommodate something like this:
(In chronological order...)
A player knows he/she will get a superpower, self-defined or not.
Their character does not have a superpower at the start -- it's just not in character design.
The player moves the character through an environment/situation.
Through a GM's reactions (that last E in IIEE), the character discovering their powers,
And the player discovering the power's rules -- learning to game within them.

My specific questions:
1. Has anyone already played this/seen this in action?
2. Is the play experience I'm describing a result of a good system or a good GM?

(To keep us from quoting Mr. Edward's brilliant "System does matter" essay, think of the second option in No. 2 as an extension of "Now your character is turning into a werewolf" situations.)

I'm not sure I understand this question, or how it relates to IIEE.  It sounds like you're applying IIEE (a way of describing stages in a conflict) to something that's much larger in scope than it's usually used for.  Can you give us an example of what this would look like in play?

Cheers,

Simon

Michael S Miller's very satisfying superhero rpg: With Great Power.

Vincent Baker's well-regarded western rpg: Dogs in the Vineyard.

Both games address what you're talking about in their own way. They're both very educational.