Whoever can collect and re-author all the special features together will be my hero! No way am I buying this movie four times.
I'm thinking a custom-made fan version of Into Darkness could have the theatrical version of the film itself & the "enhanced commentary" version on Disc 1 (too complicated to do seamless branching since the iTunes version is 30 mins. longer and rewinds stuff, just do two separate movie tracks), and all the bonus features like "making of" featurettes, deleted scenes, trailers & TV spots, production photos, etc., can be on Disc 2.
When it comes to deleted scenes, so far only the "shower scene" has been made public, and it's only available online.