These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Justice League: Doom
Complete Monster: Vandal Savage is a conqueror with genocidal plans for the planet. He manages to steal the protocols that Batman designed to defeat the Justice League in case one or more members of the Justice League turn evil. Savage makes these protocols more lethal and sadistic and then uses them to take out the Justice League. After his Legion of Doom seemingly triumphs over the Justice League, Vandal Savage informs them he plans to conquer the world by using a missile that will cause a solar flare that will kill half the world's population. This event will also render the rest of the world's population so weak and helpless that they will naturally accept his leadership.
Foe Yay/Ho Yay: There's a brief scene where we see Cheetah describe Wonder Woman as "so hot". It's not actually Cheetah saying this, just a civilian who looks and sounds like Cheetah because Wonder Woman is hallucinating. But the subtext is there regardless, and there's nothing to suggest the civilian was a guy...
Fridge Horror: When Wonder Woman tore off Cyborg's arm, SHE STILL THOUGHT HE WAS CHEETAH! There is a reason you don't see what she sees when she does that.
More so the fact that she was willing to do it, despite the fact that Cheetah and Wonder Woman's rivalry is rarely given much explanation or backstory.
Though she did apologized after she tore it off and offered to help "her" get medical aid.
This also begs the question of how many average humans (civilians and cops) were just pummeled half to death by a crazed superheroine. Their limbs aren't quite as replaceable.
Genius Bonus: When J'onn is told that poison he drank is largely magnesium which will sweat out through his skin, it creates a special Oh Crap for the audience who knows that that metal is special in that it's flammable. Magnesium flames also can't extinguished by water.
It Was His Sled: Anyone who's read Tower of Babel will know that the movie ends with Batman quitting the League.
Nightmare Fuel: Bane's attempt to kill Batman: Beating him unconscious, then burying him alive in his parent's casket, with their remains still there.
Ma'alefa'ak's assassination attempt on Martian Manhunter, and that he expected J'onn to burn for weeks.
Strawman Has a Point: Batman's contingency plans may seem extreme but his quote at the top of the page is true. How can you have a group of basically Physical Gods and not have a way to keep them from becoming a danger to humanity?
More of a subversion, since it isn't made clear that Batman is a Strawman or that we are supposed to disagree with him. In most stories, Batman is presented as the moral paragon of the DC universe.
We also have to take into account the fact that Batman makes it clear that his plans were to disable the League, not kill them. He then explains that Savage took the basic plans and made lethal versions of them. This is in contrast to the comic, where Batman's plans were much more fatal and made that way by design, meant to be implemented if Bruce was ever going against a Justice League member in a me-or-him style fight.
One of the producers narrating a making of documentary on the feature remarked that Batman had the right idea but his execution was wrong.
Tear Jerker: Two stand out moments— Bruce being buried alive in the same coffin as his parents' corpses and having to punch his way out, and Green Lantern's method of being taken out is to make him think he killed two people by making a bad call. His soft weeping will have you in tears within seconds.
The Justice League's Darkest Hour montage: Superman falling after being shot, Batman being buried alive, Green Lantern left broken and sobbing, Martian Manhunter burning in agony, Wonder Woman slowly exhausting herself fighting the "Cheetah's", and Flash gradually stumbling as he tries to keep the bomb on his wrist from detonating. The music played during the montage doesn't help.
They Changed It, Now It Sucks: Some fans have expressed unhappiness at the decisions to replace Aquaman with Cyborg, Kyle Rayner with Hal Jordan, Ra's al Ghul (The Big Bad of Tower Of Babel) with Vandal Savage and the Legion of Doom, and the the omittion of Plastic Man. The fact that, despite Michael Rosenbaum voicing the Flash, that it's Barry Allen and not Wally West (whom Rosenbaum voiced before) has also taken some people aback. Some fans who were introduced to the Green Lantern through the animated Justice League also were left with the short end of the stick with what could feel like a random replacement of Hal Jordan for John Stewart, despite Stewart not appearing in "Tower of Babel".
Also the name was changed from Tower of Babel to Justice League: Doom, however, this was a edit that was changed by TMS to avoid legal issues with Namco Bandai (link of the game here).
Lois Lane sports a starkly different model than other productions or comics, for some reason having Wonder Woman's distinctly Greek features, which has met with confusion and occasionally scorn from fans.
A lot of fans also hate the changes made to Batman's failsafes, in particular the Green Lantern and Flash traps (which were appropriately the most radically changed of the lot).
Unintentionally Unsympathetic: Batman. While we're probably meant to sympathize with Batman's stance on having contingency plans to take down heroes who are practically gods among men, he's such a nasty jerk about it that it's hard to side with him.