The Ultimate suite had to do with Cancer or curing Cancer and Peter/Eddie's father, if I remember correctly--that's just too much backstory for this film, too much involvement between Peter/Eddie. The symbiote coming from a meteorite or space shuttle, studied by scientists, is an easier route take. Plus, isn't one of the symbiote's main attractions is that it doesn't come from this planet?
Or they may have a different origin altogether, I personally don't like any of the origins from the comics (Ultimate/Secret Wars). I still think that the 90's cartoon pulled off the best origin. Perhaps it'll be a combination of the Ultimate comics and the 90's series, we'll just have to wait and see.