Either 2 or 3, leaning towards 3.

Number 3, is very "Butterfly Effect"-ish which I love. Messing with the time-space continuum is a fascinating subject. Heck, it'd be cool to go back in time and teach Einstein about the Theory of Relativity and time...the implication being that it were his theories on the subject that made it possible, but his basis for those theories came from being taught by someone from the future. Screw the spoon, there is mo chicken or wgg...

Personally, I would like to see a deviation from the traditional acquisition of super powers (accidents, experiments, and radioactive spiders) and see "super powers" as the result of harnessing the untapped potential of the human brain, sort of like John Travolta in Phenomenon. This allows the audience to relate more strongly with the subject and characters because its more feasible for it to be anyone; any human on the planet can become in other words extraordinary, you just have to be able to tap into those latent abilities. I keep thinking of Lawrence Fishburn in the Matrix saying "there are those who are so hopelessly dependent on the system that they will fight to protect it." The key then, would be to break free from the confines of the system.

2 or 3. I do agree with Zhammy that 3 is very Butterfly Effect, but like him I do love that. But I'd just be careful not to mimic it too directly.