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.
Alternative Character Interpretation: Is Batman the Only Sane Man for undertaking an unpleasant but necessary task of creating plans to disable and/or destroy his Justice League allies, or is his arrogant, Never My Fault dismissal of his allies at the end as he storms out and quits the League like a spoiled child who cares more getting his way than he does about people and blatant insensitivity to how betrayed the other heroes feel indicate that he's just an immature, emotionally detached, Psychopathic Man Child who is simply too out of touch with his humanity to understand anyone?
Base Breaker: Was Batman fully justified in his actions, or was he a nutjob effectively planning to murder his closest allies with very flimsy reasoning?
Big Lipped Alligator Moment: Ten repeatedly hitting Superman in the face, only to have his blows bounce off of Superman ineffectually, eventually breaking one of his hands, and then having his other hand crushed by Superman before the Man of Steel smashes him to bits. Superman fans may love seeing Superman being an immovable object here after all the times he had to be a jobber in past animated Justice League features, but it's not particularly funny or impressive.
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...
Ma'alefa'ak attracts Martian Manhunter's attention by taking the form of a seductive blonde woman and buying him a drink. He acts no less seductive even after J'onn finds out who he is. Did we mention they're brothers? (even if the movie itself didn't)
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.
Mood Whiplash: The montage of scenes showing the League defeated or slowly failing are quite tragic. That is, until the camera pans to Martian Manhunter running around on fire, screaming at the top of his lungs. The action was so over the top that it's actually kind of funny.
Narm: As seen in Mood Whiplash the montage of scenes showing the League in defeat is more funny than tragic, especially Superman's rather over the top fall after being shot by Metallo.
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.
It's also important to remember all the times the League's members (both individually and as a group) have had their powers stolen, been cloned, succumbed to mind control, etc. Pretty much every single one of them has had all of these things happen at one time or another.
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 omission 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).
They Just Didn't Care: There's a very strong sense of been there, done that with this feature, made all the more apparent by the painfully lackluster fight scenes, most of which pale in comparison to similar hero/villain match ups done in previous DVDs or even done in the DCAU. The Justice League Vs. Royal Flush Gang fight in the opening doesn't have half the energy from the Wild Cards episode of Justice League, despite that episode being done over ten years earlier on a much smaller budget. The Superman Vs. Metallo fight at the end isn't half as brutal as their fight in Superman/Batman: Public Enemies, or even their fights in the mid-90s DCAU Superman series. Batman Vs. Bane ends the way it always ends - with Batman yanking that damn venom pump out of Bane's head. The only fight that really stands out is Wonder Woman Vs. Cheetah, a fight the animation team at WB have undoubtedly wanted to do for years.
It doesn't end at the fights either - Superman getting shot by Metallo with a Kryptonite bullet and then falling from a great height was done previously in Public Enemies, Legion of Doom shout outs were done in Justice League Unlimited, etc. Hell, even the voice actors, mostly DCAU veterans (with Nathan Fillion being a hold over from the Emerald Knights DVD) sound bored with their work.
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 (even after he gets buried alive with his dad's corpse).