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.
Anticlimax Boss: After the Gibborim were summoned to Earth in the "Lost and Find" storyline, seconds later they are held at gunpoint by Phantom Zone-based weapons (that had previously nearly wiped them out in the past during their war against Krypton) and Superman gives them the choice of returning to where they came from or fighting a no-win scenario. They immediately chose the former without hesitation.
Boring Invincible Hero: A criticism levelled at Superman, and justifiably. He doesn't meet a real challenge until he goes up against General Zod.
Character Shilling: For both Clark and Allison, throughout the first three books in particular. Clark was, to some degree, understandable, being Superman. Allison, on the other hand, became The Scrappy, though she may have been Rescued from the Scrappy Heap by the events of Book 3. The jury is still out.
Gary Stu: It can be argued that Superman is too good than any of his media portrayals, namely that he is not only a superhero but is also too well-knowledge in Kryptonian science, often being a Deus ex Machina, have a celebrity girlfriend, and commanding a Kryptonian Kill Sat along with a fleet of Cool Starship.
Growing the Beard: While good to start with, the series has grown from a simple X-Men Evolution/Superman crossover with a flair for background detail in which everyone was essentially a cheerleader for Superman's awesomeness into a complex, tightly woven and cleverly plotted story in which characters are more balanced, Character Development is well handled and everyone gets at least one Crowning Moment of Awesome.
Narm / Narm Charm: yo-yo's back and forth between these, with the slightly cartoony and over the top narration and the generally cheesy nature of some of the dialogue, particularly in the earlier stories.
Rescued from the Scrappy Heap: Alison Blaire, more or less. Having previously been an annoying Mary Sue, her discovery of some of her Dark and Troubled Past her mother was Madame Hydra, who seduced Alison's father simply to get at his dna, worked with Mister Sinister to ensure that the baby had the necessary powers and appearance, aborting over half a dozen pregnancies in the process. She even faked a career in music to get Alison to go down that path. In essence, everything about Alison was a lie which led to a thoroughly effective Break the Cutie, and deal with it herself in a thoroughly realistic and awesome way did a lot to endear her to fans.
What an Idiot: Duncan stupidly punched Superman in the face when it was clear his attempts at racist bullying weren't working...and broke his hand in the process while Superman was completely unfazed.
Cadmus fiddles with a piece of Kryptonian technology despite not knowing anything about it, and end up nearly dragging the Earth into a black hole while also causing the release of General Zod.
Though it was Mary Storm who was responsible for tampering it.
The Friends of Humanity in general fall into this trope due to several factors, including countless examples of Bullying a Dragon, having no members within their ranks who can match the heavy-hitters of the Justice League in a fight, severely overestimating humanity's opinion of them, having comparatively primitive weaponry, and being overall dumbasses in general. Really, it's a wonder how they lasted as long as they did when, compared to the Big Bads of the series, they're nothing but a joke.