Alternate Continuity: The game branches off from the manga after chapter 31, and makes a few rather important distinctions. The character Father, introduced in the same chapter, is Hoenheim. The homunculus known as "Pride" does not exist yet. Bradley has a son named Selim, who is his biological son.
Big Screwed-Up Family: The creator is the homunculi is Hoenheim, father of Ed and Al, which also makes the homunculi their siblings.
Bittersweet Ending: Two of them. In the Roy ending, Alphonse dies and Edward is heartbroken; but life goes on, Roy becomes Fuhrer while Ed ends up as a General and they even start dating. In the Veggie!Ed ending, Edward sacrifices himself to save Alphonse and ends up in a vegetative state.
Came Back Wrong: Pride, in stark contrast to Edward, is (arguably) as heartless and cruel as the rest of the homunculi. His mental state initially appears to be that of a Type-1 but quickly shows signs of being a Type-2, although physically he is somewhere between a Type-3 and a Type-4.
Collapsing Lair: In the Pride!Ed ending, Edward's alchemical rebound causes the Homunculi's lair underneath Central to explode and collapse. In an inversion of the trope, he's the hero and did it completely by accident.
Composite Character: Taking advantage of their similar look in the manga, Hohenheim and Father are one and the same. Not much had been revealed about them in the canon at the time that Bluebird's Illusion was made, so anybody could have guessed that Father and Hohenheim were the same person. (Eventually it was revealed that they were completely separate characters, although they did still have a relation.
Dead Fic: There was once a fan comic being made based on the game (the cover is the page picture), but it has since been discontinued and its website taken down.
Downer Ending: The Pride!Ed ending. Roy Mustang and Al are accidentally murdered by Envy when they try to protect Ed. The heartbroken and insane Edward fights King Bradley to the death and wins, but is left to die in an explosion he inadvertently started. However, Envy brings him before Father where he is "reborn" as the homunculus Pride.
Failure Is the Only Option: There is only one happy ending, and it's a joke ending. This trope also applies to the Big Bad, who suffers a serious setback in each of those bad endings.
Fan Nickname: The titles of various endings. "Tea Alchemist ending," "Pride!Ed ending," "Roy ending," and "Veggie!Ed ending."
Fanservice: The scene where Alphonse is showering, and the scene where Al finds a photograph of Ed in a dress.
Happily Ever After: Parodied in the Tea Alchemist ending. Edward is renamed to the "tea alchemist" and he must serve tea to King Bradley.
Heroic Sacrifice: In the Veggie!Ed ending, Edward sacrifices himself to save Alphonse. In the Pride!Ed ending, Roy and Al sacrifice themselves to save Edward.
James Bondage: During the latter part of the game, Edward is kept prisoner by the Homunculi, and is cruelly beaten, tortured, and generally abused by Envy. Later we learn that the Homunculi are Ed and Al's "siblings," which increases the Squick factor a whole lot.
Jossed: The game predicted that Pride would take over Edward's body. In the manga, Pride tries to take over Edward's body, and fails to do so.
The game also predicted that Father was Hohenheim. Not quite, guys.
Justified Title: The "bluebird" in the title refers to the Elric brothers' happiness. Hence their new, happier life is merely an illusion preceding the horrible fate in store for them.
Luke, I Am Your Father: After Edward is held captive in the homunculi's lair, he is introduced to the Big Bad, who turns out to be his own father, Hoenheim. Alphonse learns the same thing when he infiltrates the lair to save Ed.
Sole Survivor: In the Pride!Ed ending, Riza's the only one of the main protagonists who's still alive and healthy, although she misses Roy and the Elrics badly. While Edward survives, he also comes back wrong.
So Proud of You: Hoenheim refers to Edward as his "most perfect son." In the Pride!Ed ending, because Edward exceeded all his expectations, he orders Envy to save Edward from being Buried Alive and rewards him with "a new life... a perfect, immortal life."
Spell My Name with an S: The intro movie refers to King Bradley as "King Bradrey". One online translation also names his son "Samuel" rather than Selim.
Time Skip: The game takes approximately one year after chapter 30 of the manga (or alternately the first season of the second anime). In that time, Edward has gotten a new body for Alphonse, Riza has bought them a house of their own, Roy has been promoted to General and Edward to Colonel, and the characters have gotten past Hughes' death.
Utopia Justifies the Means: Father seeks to create a world free of human greed and claims all humans are marked with "inerasable sin." To this end, he enlists Edward to turn the people of central into a new Philosopher's Stone.