Re: The Official Scarlet Witch Thread
When I was first exposed to Scarlet Witch - courtesy of some hard-bound Avengers graphic novels that were part of the library collection at one of the elementary schools I attended - I had no idea she was a mutant, let alone the daughter of Magneto, so I don't think it's going to be that big of a deal to work around the 'off-limits' aspects of her character or that of her brother's.
Given that we're going to see Doctor Strange show up in Phase 3, I think the supernatural angle, as suggested above, would actually be an excellent way to explain her abilities. As for her brother, I think a technological-based angle - or even the 'super-soldier serum' explanation would work best for him, although you could bolster SW's character and powers by saying, as suggested above, that she cast a spell on him to give him super-speed.
I also wouldn't put it past Joss to make one or both of these two the bad guys.