Most remastered games, movies, etc, usually keep all the original content, and just redo the textures and pre-rendered movies in HD. Kind of like remastering an old TV show from DVD to Blu-ray. Same exact show and content, just better resolution. Nothing changed though.
The scene where the Crucible docks with the Citadel is one such example of a pre-rendered movie. Maybe throw in an HD audio track for the music. They don't completely change the experience. I expect the remastered version will have the same ending, choices, and all the DLC included.
There's a difference between remastered, and reimagined.
An ending which allows you to defeat the Reapers on your own terms, despite the game not giving you the option, is a reimagined version.
An ending which expands on scenes (Shepard in the rubble) or removes certain parts (Godchild, Crucible plot), despite the original game or DLC not doing this is a reimagined version.
A remastered version is much like my example I used in the first paragraph, and is more likely what will happen.