What major actions or choices determine the alternate storyline/endings in Batman: Arkham Knight? I also have all the DLCs you can get for the game for example, the batmobile/character skin packs as well as the extra storylines, such as the Harley Quin and Red Hood sagas. So does completing certain missions or sections of the storyline wearing any of the different skins/costumes or certain decisions/choices have anything to do with altering the game or ending, add extra side missions, or unlock anything in the main story line?
I've finished the game twice, and have seen no indications of any alternate endings for wearing alternate costumes (though it's possible that some of those costumes may make for some amusing cutscenes). I also don't recall any decisions that can be made substantially differently - the plot is highly linear, with the side missions being largely independent of the main story. (Some characters in the side missions play a role in the main story, but their side mission will only become available once their role in the main story is complete.)
There is an "alternate" ending for completing all side missions that comes in addition to the "basic" ending, and is more final. And there is DLC that is set before that final ending in the timeline. If you get that final ending and then choose to go back and complete that DLC, the game simply sets you back in town before that final ending. (This is also the case if you want to go back and complete a few achievements.)