Accidental Aesop: Jun's relationship with rival Aoi Kurosaki can be for a realistic depiction of the Loving Bully growing up. While Jun does not wish ill will towards Aoi when they meet again and learns Aoi's horrible back story, she also remembers how Aoi treated her when they became rivals and at worst was an arrogant jerk to Jun. When Aoi returns after recovering from their first fight and becoming a fellow Human Alliance member, Jun has in the meantime been reminded of all the bad ways Aoi was rude to her growing up and rebuffs her romantic advances. Yes, people can be confused by their emotions and ultimately realize that they in fact are attracted to a person they bully, but their victim may not be receptive to their feelings and will remember how they felt while being bullied over their bully's new feelings of attraction.
Arc Fatigue: A common complaint is that at too many points the manga seems to go on what appears to be its final arc only for it to reset status quo and return to Monster of the Week format again.
Ensemble Dark Horse: The Archangel Michael is the most popular character in the manga and is often included in fanworks of the original Devilman.
Mita, the Devil Beast boy known as the Mouth of Truth, escaped alive from his encounter with Jun and was apparently setting to become a vigilante on his own. However, he didn't return afterwards and was never mentioned again.
Jim Langer/Devilman Liger seems to be an important character when he's introduced in the fifth volume, but he basically disappears afterwards and doesn't return until the last volume. His role as the Human Alliance's second Devil Man and his interesting relationship with Jun are points some feel should have been more developed.
Too Bleak, Stopped Caring: With 17 volumes chock full of dismemberment, rape, trauma and all sorts of monstrosities, it can become a bit tame for the reader at some point.
Viewer Gender Confusion: Unlike most of GO Nagai's work, this one gets a surprising subversion. (And a complete aversion in the anime adaptation)
Lan Asuka, unlike in the manga, is revealed to have been manipulating protagonist Jun Fudo the whole time. First awakening Jun's powers as a monstrous Devil Beast by letting another attack and try to rape and eat Jun, Asuka forms a lust towards Jun's alter-ego of Devilman Lady and constantly toys with her and her friends. Asuka manipulates conflicts throughout the series between humans and the mostly peaceful Devil Beasts, resulting in camps formed to hold and exterminate all the Devil Beasts. Asuka lures Jun to her and reveals her true intent: Despising the world and all in it, Asuka, who had been born both male and female, wants to use Jun to become a new God of the world. Asuka paralyzes Jun and then, demanding Jun "prove" her love for Asuka, rapes a traumatized and terrified Jun before informing her Jun had been born solely for her and would now die for her before disposing of her. When Jun returns, the newly deified Asuka mocks her, saying being perfect was too good for a "hideous creature" like Jun before trying to destroy her in their final battle. Valuing her own ego above all else, Asuka is a manipulative and cruel embodiment of lust and selfishness.
Satoru, the seemingly young leader of the militant Devil Beasts, is an absolute sadist who believes in the genocide of humankind. Devoting himself to the supremacy of Devil Beasts, Satoru inspires the awakening of them as feral beasts who slaughter those around them while masterminding a series of brutal terrorist activities that claim many lives. With no patience for Devil Beasts who fail to embrace his fanaticism, Satoru sees them as enemies to be annihilated, especially Jun Fudo, who Satoru dedicates himself to destroying mentally. Satoru, at one point, abducts and brutally murders Jun's friend/Love Interest Kazumi while mocking her over the death of "one human", before attempting to finally kill Jun himself. Sinister, cruel and monstrous, Satoru shows that he and Asuka are simply two sides of a dark coin.