Since it's clearly said that in Season 2 of Flash, Barry will enter in Parallel universe. So there will be changes in Arrow's story line too.
Oliver dies with ship sink, instead his father survived and became the Arrow.
He then decides to right his wrongs so that he can honor his son's memory.
Slade Wilson and Oliver were never friends. They always remain enemies. In-place of Oliver Slade was given "the choice" whom to save.
Due to injected by Mirakuru Roy kills Thea.
Flash and Arrow have a combat just to prove each other that the other one ways of dealing with their enemies is wrong.
Watching his father killed by Arrow. Tommy decides to take revenge from the Arrow.
Oliver actually kills Diggle in the fight to prove Ra's his loyalty.
In place of Thea, Felicity gets killed by hands of Ra's and she is taken to the pit for rebirth which makes her forget every recent thing happened in her life.
Instead of Ra's, Damian kills Thea to make Oliver heir of his throne.
We may see story of Arrow just like we read in comics.
That's all my prediction are of Arrow of Earth 2.
For Earth Prime I believe that Damian will kill Thea or Felicity to bring Oliver back as Arrow because he was having no fun while wandering in city
or there maybe a possibility of Nyssa joining the Hive to gain his father's throne and then taking revenge on Oliver by punishing his beloved one's.