[[WMG: The Penguin was not kidding…]]
…the whole movie is Max Shreck's nightmarish DyingDream. In the dream he does things like giving in to his long-held impulsion to kill his obnoxious secretary, and he also sees his old business rival Bruce Wayne as Batman, because… why not? Both their names begin with B! And then there's the stuff that's just plain DreamLogic only a feverish brain could cook up, like [[CrazyAwesome the steampunk bomber-penguins]]. This also serves to explain why Shreck looks so indescribably nonplussed-but-mildly-surprised throughout the whole movie — that's very much the face someone would wear while half-consciously living through a particularly weird nightmare.

[[WMG: Catwoman is a Lannister]]

"Hear me roar." Also, hair color fits.

[[WMG: [[ComicBook/AllStarBatmanAndRobinTheBoyWonder Crazy Steve]] replaced Batman for most of the film]]

The Agony Booth review suggested this, but it would actually explain the film's inconsistencies. In the first film Batman only killed one person in extreme self defence, never seemed to enjoy it and even tried to save Jack in the chemical plant. In Returns he goes out of his way to blow up mooks while grinning. After the Batsignal summoned him Steve intercepted Bruce, knocked him out and stole his suit and took his place up until the third act. Bruce eventually took him out, which is why Batman is suddenly against Selina killing the man who murdered her in cold blood despite being a ok with blowing up some random goon for giggles. In fact Bruce was so ashamed of what Steve did he completely forswore lethal force for the rest of the series.
** Or it wasn't until seeing someone else going down the same path that he realized how far he'd fallen and turned away from it. He even warns Robin away from following that path in the next one.

[[WMG: The infamous missing eye makeup was no mistake.]]
Batman has been known to look different from the perspective of others, the guilty see nothing but shadow especially around the eyes. Whilst the innocent do see the clear face since they have nothing to fear from him.

[[WMG: The Penguin murdered his parents, then ''pretended'' to discover their graves.]]

This is actually not so much a WMG as a legitimate part of the movie, which becomes increasingly clear if you [[AllThereInTheScript look over the script]] or [[AllThereInTheManual read the novelization]].

[[WMG: Chip Shreck would have become a villain in ''WesternAnimation/BatmanTheAnimatedSeries''.]]
Originally Max was intended to appeared in the cartoon where he apparently survived his ordeal with Catwoman, before they created [[CanonForeigner Roland Daggett]] instead. But since Max is clearly dead, it seems more logical that his son take up the role. The death of his father would have contribute to his slide to villainy, since he's already [[TurnOutLikeHisFather like his father]] (as he's aware he pushed Selina out the window).

[[WMG: Bruce Wayne is a coulrophobic [[FantasticRacism Fantastic Racist]].]]
Why is Batman so unnecessarily brutal in dealing with the Red Triangle Gang, to the point of [[MurderIsTheBestSolution outright slaying two of its members]]? The answer, of course, is because they're clowns (well, most of them, anyway), and it had been established that Bruce Wayne has serious issues with comical white-faced characters. Recall the scene in the 1989 film when he's at the steps of the courthouse and shoots a DeathGlare at those mimes; this is before he knows they're working for ComicBook/TheJoker, and even before he knows that the Joker exists! It makes it hard not to wonder: perhaps Jack Napier ''didn't'' kill Thomas and Martha Wayne. We're never told exactly what kind of movie the Waynes went to see that night. Perhaps it featured a particularly terrifying MonsterClown as its villain, and young Bruce naturally conflated that memory with the one of his parents getting shot. So when Napier suffers an accident that turns him clown-faced, Wayne makes him a scapegoat for the tragedy, [[SelfServingMemory conveniently "remembering"]] that the murderer also made the "pale moonlight" reference when in fact this is a rationalization his mind made up! Now Wayne just hates all clowns, or anyone who ''looks'' like a clown, and if they're criminals - even relatively harmless ones - they deserve to die.

[[WMG: Max Shreck is the Penguin's older brother.]]
Based on a draft of the script.