Broken Base: The general plot point of Barry saving his mother from Thawne is continuous. Supporters on this say that Barry's actions were selfish and thus had to be punished. Detractors, however, point out that Thawne killing Nora Allen and framing Henry for it was itself a change to the timeline as they were originally alive and able to enjoy their son's success as the Flash until Barry's return in Flash: Rebirth and thus Flashpoint shouldn't have even happened at all because Barry was only undoing the damage Thawne did. Another faction point out that, as understandable as Barry trying to save his mom was, the way he went about it was incredibly stupid. He knows Thawne is dangerous and that previous attempts to alter the past have ended badly, so the smart thing for Barry to do would've been to reach out to his friends and allies who do have experience with time travel in order to undo Thawne's sadistic alterations. In this sense, Barry's decision to save his mother was an incredibly stupid and selfish one because he thought he could fix it by himself when history tells him he should know better. Especially grating because Barry just recently needed to take Thawne down with help from the rest of the Flash Family, and they'd been trying to reach out to him and remind him he's not alone in the issues leading up to Flashpoint.
Cry for the Devil: This universe's Joker seems to be even crueler than the normal universe's Joker, reaching The Dark Knight levels of Cold-Blooded Torture, including turning Selina Kyle into a quadriplegic and tricking Jim Gordon into murdering Harvey Dent's daughter. And then you find out the Joker's identity: Martha Wayne! As well as the reasons why they came to be.
Darkness-Induced Audience Apathy: Between the massive bodycount, the relentlessly Crapsack World, and the whole thing taking place in an alternate universe so it doesn't matter anyway, most readers find Flashpoint very hard to sit through. And that of course not taking into account the massive anguish of Flash through the story due to what he accidentally did. Even in the backstory, it's abundantly clear that the plot only works if the vast majority of characters are extremly OOC or needlessly aggressive. Which really just makes the event feel ingenuine in addition to depressing.
Eight Deadly Words: One reviewer about the event. It's hard to care about the events of an alternate universe that wouldn't exist or matter anyway after a few months. It's harder still when the overwhelming majority of the characters are so hideously unlikeable that you get the impression the world would be better off destroyed. Add in the fact that the only character from "our" DCU is Barry Allen, widely regarded as a Creator's Pet, and you have a comic that winds up mostly being a lot of empty, unpleasant noise.
Ensemble Dark Horse: Frankenstein and the Creatures of the Unknown received a lot of praise as well.
"Funny Aneurysm" Moment: In the miniseries Batman: Death and the Maidens of the original universe, Bruce once hallucinated meeting his parents after drinking an elixir. They both disapprove their son's costumed crusade. However, Thomas was more understanding, and was mostly unhappy that Bruce has to give up many things to become Batman. And yet here, Thomas is the one who is Batman...
Other than Sandman's appearance in the first issue, he pretty much disappears from the rest of the series and his only appearance holds absolutely no importance or significance on the rest of the series. It makes you wonder why he was included at all.
Blackout was on the run from the Outsider, whom he claims "ruined his life" because his corporation's been trying to hunt him down and use him as an endless supply of clean electricity to power India. But during the Outsider's tie-in miniseries, Blackout doesn't get any real focus beyond rehashing his dialog in Flashpoint #1, and instead the bulk of the conflict is between the Outsider and Martian Manhunter. What's especially grating is how new character Canterbury Cricket managed to get an entire one-shot dedicated to him when he didn't even appear in the main series until it was halfway over. And finally, when Blackout, the Cricket, and the rest of the Resistance appear in the last issue they're immediately killed by Enchantress just so Subject-One can stop her.
Not to mention the Outsider himself, a super powered and stylish Magnificent Bastard who would make for an equality interesting protagonist or antagonist in the post-Flashpoint DCU, but it seems we've seen the last of him.
Muchhead-slappingensued when the Flashpoint world map was released and people saw that most of Africa is listed simply as "Ape-controlled." Apparently no one at DC thought this might be taken badly when applied to a continent overwhelmingly populated by black people, given the historical tendency for black people to be likened to monkeys and apes in racist propaganda. For the record, "ape" in context refers to Gorilla Grodd, a previously established Flash villain who is literally a gorilla, but the fact that this is the only information we had on the entire continent (besides the fact that a large part of Northern Africa is missing due to the same war that destroyed most of Europe) was the real unfortunate part, and the fact that Batman: Incorporated had done something similar with the "Batman of Africa" (falling into an unfortunate tendency to treat the entire continent like it's one country) a few weeks earlier did nothing to help.
Additionally, a variant cover that was released that showed Wonder Woman holding Mera's decapitated head drew controversy due to its blunt visual (ironically said cover is speculated to be a homage to a similar cover of Crime Suspenstories that was used as an example of bad taste that eventually lead to the creation of The Comics Code).
Superman. He crash-landed in Metropolis as a baby, accidentally killing thousands. Then he spent his entire life locked in a lab where he was no doubt experimented on for decades. Rockets for Krypto & Kara eventually arrived, but from the looks of it, they've fared worse than Kal-El (KRYPTO IS DEAD & A FREAKING SKELETON WHEN BARRY FINDS HIM!!). He hasn't known any human kindness nor contact for decades. The only person to threat him like a person was General Lane who treated him as a son and more than an experiment, but he got pulled into the Phantom Zone when Clark was a child, while Krypto was put down for mauling a young Lex Luthor.
Selina Kyle, Oracle. Almost totally paralyzed from a vicious attack by the Joker, she's unable to even wipe the tears from her eyes as she relives it.
Harvey Dent's son, who gets kidnapped by the Joker along with his sister, then has to watch his sister get killed by Jim Gordon because she was dressed by the Joker. And later, he has to watch the Joker kill Jim right in front of him.
Barry Allen also falls into this territory. All he wanted to do was save his mother from Thawne, but he unintentionally creates a Crapsack World. His options aren't so great as it either consists of letting his mom live but everyone else dies, or return reality back to its intended state but his mom dies. Not an easy decision there.
Americans Hate Tingle: To put it simply, the show isn't nearly as popular in the U.S. as it is in Canada despite its support from CBS.
Awesome Music: The songs that play over the last few minutes of each episode tend to be pretty fitting/awesome. A list can be found here
The show's own, unreleased music is also pretty good, but sometimes it transcends to superb. During the fourth episode, Asking For Flowers, a woman has taken the abusive husband of her sister hostage; we get three variations on the same theme. First a sharp, harsh take as the husband manages to get the gun and starts choking out the woman while the team listens in. Then a longer, slower version while Parker distracts the husband with a phonecall and tries to convince him to deescalate, without admitting they know what's going on, building into optimistic as the tactical part of the team sets up their entry. Finally a drums version as he hangs up on Parker and makes as if he's going to shoot the woman, and then turning into relaxed horns to go with Ed Lane's "Put the gun down!" and the husband being cuffed and brought out.
Cargo Ship: Many people tease Spike about Babycakes and how she was his "girlfriend".
The episode "Good Cop" is about a cop who gets demonized by everyone because he accidentally shot an innocent kid. A year after that, the death of Trayvon Martin happened.
The series finale "Keeping the Peace, Part 2" is haunting considering that it aired in Canada the night before the Sandy Hook Elementary School shooting in the United States.
That episode may also be harder to watch after the Boston Marathon bombings that occurred a few months later.
Moral Event Horizon: Any time a hostage taker deliberately executes a hostage, most notably Misha Kondrashoff in "The Fortress" and Goran Tomasic (while his wife wasn't a hostage at the time, he shot her in the back, in cold blood).
Also the plane hijackers in "Grounded" where they planted a few of their own among the passengers and when someone tried to be a hero, they shot him down.
Whole Plot Reference: The third-season episode "Collateral Damage" borrows a number of elements from The Fugitive, including the plot of a wrongfully-convicted man using a prison transport crash to escape and attempt to clear his name.