Fantasy World:
I think, so long as magic is widespread in the world in that everyone [i]can[/i] use it (basically, our characters aren't the only special ones that can) but only if they work for it, we wouldn't have to worry about verging in mary sue territory. Sticking with runes and potions seems like it would work, as well. But how do we go about using runes? Like, will we stick to using magic wands to draw runes correlating to a spell? Or will we use incantations? 

Sci-fi World: 
For this, I imagine magic and science is one and the same. How do we want this world to be though? Sort of sleek with technology integrated within the world, like [url= http://simplywallpaper.net/pictures/2014/08/Guardians-of-the-Galaxy-Xandar-Wallpaper.png]Xandar[/url] in Guardians of the Galaxy, if you guys have seen it. Or more dark and gritty cyberpunk like [url= http://4.bp.blogspot.com/-4UecUsH0TDI/T0JNrEPwN3I/AAAAAAAAARI/qvgjD1hhoQE/s1600/actmm_matte_6_by_rich35211-d4lsg5v.jpeg]this.[/url]

Modern World: 
I think we could maybe integrate the prophecy and warring worlds idea together. So waaay back when, travel between world wasn't unheard of. In fact, it was a common thing to do. But then something happens, and the three worlds sort of start becoming hostile, and their conflicts just slowly develop into all-out war. As a last resort, they decide to break the mirror—which is the only means of world transportation—and from then on, each world was on their own.

As for the prophecy, it could be one that forewarns a threat to all three worlds. So it'll basically be saying the three worlds need to unite and band against this super big bad, or they'll all die. But it's been centuries, millennia, and nothing has happened. The prophecy's become like a fairy tale in the modern worlds. People know about it, but they all think it's just a story.

I do agree that it could be interesting if prophecy gets mixed up in the other worlds. Like, in the fantasy world, it becomes twisted into like a day of reckoning sort of thing. They think when the prophecy happens, it'll be the end of the world for them for some reason, so they're hell bent on disrupting it and making sure it never becomes fulfilled.