It is just a messy, silly story. Basically they need to cut the majority that has occurred. Almost all of Alpha (I love the Alpha series, but the story was full of nonsense and contradictions), with the exception of a few key aspects (Charlie's death) and the origin story of the character introduced in it (the ones that are worth keeping, at least). Cut the silly stuff from SF3. Gill being president, losing the fight with Urien on purpose so he could be secret president level two. A great deal of what occurred in SF4... Make sure to have tied up all the dangling lose ends that have been hanging around for forever (satsui no hado). Basically, the story is a wreck, it needs to be consolidated and cleaned up. I would like to be more specific, but I would actually have to research the very stupid story, my brain hasn't bothered holding on to much of it.