1) In Civil War storyline, Captain America was killed by Crossbones (Brock Rumlow) and a brainwashed Agent 13 (Sharon Carter). Both characters have already been introduced in Captain America: The Winter Soldier (2014)
2) In the original Civil War storyline, Steve Rogers (Captain America) is killed and Bucky Barnes (The Winter Soldier) and Sam Wilson (Falcon) become the new Captain America(s).
3) It was revealed that Captain America's team consist of Hawkeye, Falcon, The Winter Soldier, Scarlet Witch, Sharon Carter/Agent 13 and Ant-Man while Iron Man's team consists of War Machine, Vision, Black Widow, and Black Panther and the newly revealed Spiderman.
4) Captain America will not die in the film, as Chris Evans has two more films on his picture deal contract. After this, there are Avengers: Infinity War - Part I (2018) & Avengers: Infinity War - Part II (2019) left after them there is a possibility that Captain America will not die after all but will probably Retire at the end of Avengers: Infinity War Part, 2 and Bucky Barnes who is Captain America's old friend and used to be Winter Soldier will be trained.
5) At the end of Avengers: Age of Ultron (2015), Captain America forms new team consisting of Black Widow, War Machine, Vision, Falcon and Scarlet Witch. However, its unclear that this new team will follow Captain America or not due to Civil War between Avengers
6) Thanos will possibly appear in this movie, if not but the credit scene to obtain the Mind Stone from the possibly destroyed Vision's forehead to put on his Infinity Gauntlet.
7) Sebastian Stan revealed that the backpack that Bucky is seen wearing in the trailers contains journals that he has put together of his scattered memories
8) Spider-man is rumored to have two costumes in the film, one being his classic costume
9) Since actress Emily VanCamp has joined the cast as Agent 13, it is rumored that Steve Rogers will die, much like in the comics
10) In the comics the Fantastic 4 play a big role in the story. Due to Marvel not owning rights to them and the Fantastic 4 getting a reboot in 2015 this will not happen.
11) Mutants (such as the X-Men) play a part in the original comic book story as human society had always held a prejudice against mutant-kind while also being accepting of non-mutant heroes. When the tide turns against all powered people some characters view it as fitting since non-mutant heroes had it easy for so long and others view it as troubling. Since 20th Century Fox owns the rights to the Marvel concept of "mutants" this will not be a part of the film.