I know many of us have been wondering how Ellie regained her eye if Stross removed it in DS2. Reading the wiki and in particular an article of one of the Ishimura's decks, I found something very interesting. (http://deadspace.wikia.com/wiki/Medical_Deck#Biological_Prosthetics_Center)
The Ishimura's BPC is a location on the vessel where crew members having suffered amputating injuries may come to have a biological prosthetic grafted on. These sorts of injuries seem to be frighteningly common aboard the Ishimura given the size of the BPC. The biological prosthetics are apparently created by means of cloning the individual, rapidly aging the clone to adulthood and then harvesting the prosthetic limb or organ from the clone; no mention of how infant clones are grown to adult size in anything resembling a speedy manner.
This text, plus the fact that are 1 or 2 more people with Isaac and Ellie in the trailer, makes me think the following facts:
1.- DS3 takes place months or even 1 year after DS2; and 2.- Ellie made a clone of herself, and transplanted the eye of her clone to herself.