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.
Then subverted in issue 7, where, when all the action has died down, and he is no longer needed to save the world, Alan can mourn. He breaks into a Heroic BSOD, and wrecks their apartment.
Base Breaker: Batman and Superman stealing the show. Instead of focusing on Earth 2's unique heroes, which made the book successful, the Dark Age arc is pretty much Injustice: Gods Among Us set in Earth 2. Evil Superman wants to take over the world by force, Batman gathers and leads a Resistance to fight him. Everything revolves around Superman and Batman. While part of the fans enjoys the Dark Age arc, the other part feels that it hurts the book's uniqueness and turns it into just another Batman/Superman title. This focus continued into the following arc, which was named "The Kryptonian" after someone who was not involved in the aforementioned feud.
Ho Yay: A bit between Jay and Khalid in issue 11, Jay was Khalid's inspiration to endure the insanity to become Doctor Fate, despite only formally meeting Jay a few hours ago.
Misblamed: Some fans don't like the return of Batman and Superman and blame new writer Tom Taylor because he took over writing duties after The Reveal. However, both characters were reintroduced by James Robinson, the original writer.
Moral Event Horizon: In issue 25, Kal-El's murder of Jonathan Kent in the name of Darkseid cemented that there is no turning back for him, and was intended as that point by the writers, who see it as when "Clark Kent" ceased to exist in favor of Kal-El only.
However, it turns out that it wasn't Kal-El that crossed the line. It was a clone created by Darkseid that had Superman's memories.
Tearjerker: The origins of the Furies of Apokolips. Unlike the traditional Female Furies, who were born and bred on Apokolips, the four Furies were drafted into Darkseid's service. Pestilence and Death had the most heatbreaking stories of all:
Pestilence had to endure the death of her parents due to the negligence of the upper classes on her home world, who then pumped her full of diseases and dumped her on Apokolips, all so that they wouldn't have to dirty their hands keeping their planet safe.
Death had to witness her daughter's murder. Her grief was so crushing that she was willing to copulate with Darkseid so that she could be a mother again.
The Untwist: Batman II's identity? Thomas Wayne, of course. It's pretty much got to be, since a black-and-red lethal force-employing stubbly legacy Batman already appeared in Flashpoint, where he was also Thomas Wayne. It didn't help that DC spoiled his identity in a tweet previewing several Earth 2 action figures months ahead of the actual reveal, also confirmed by Robinson after he jumped ship from DC.
They Just Didn't Care: Earth 2: Worlds End has multiple artists and writers working on each issue, and as a result, the editorial often misses out on discrepancies, sometimes in the same issue. One example is Dick and Barbara Grayson's son, whose name is either Johnny or Tommy, and whose hair color changed from red to black within a single issue.