* ArcFatigue: Unfortunately went down this route after sometime, since the arc later separated into several mini-arcs for a while until ending in ''War of the Supermen''.
* CharacterDerailment: General Lane and [[spoiler: Lucy Lane]] being suspicious of Kryptonians? Fine. Both wanting to commit ''genocide'' against them for no crime greater than existence? Fans were not amused.
* CompleteMonster: Reactron, a SociopathicSoldier who threatens to rape Supergirl, kills a number of Kryptonians, including her father, tries to murder Mon-El in order to frame Krypton, depowers Supergirl and Flamebird and tries to sexually assault them, and finally blows himself up in the heart of Kandor, killing Supergirl's mother and ninety thousand+ other Kryptonians, gloating the whole time.
** Brainiac, who destroys one planet, tries to destroy Earth, kills several thousand Kryptonians, kills Jonathan Kent, and attempts to melt Superman's brain by feeding several world's worth of information into it.
* MagnificentBastard: Luthor is at his best here, cooperating with Lane to achieve a goal he would have worked towards anyway, playing Brainiac and Superman alike to his own ends, and ultimately being rewarded for his role in [[spoiler:destroying New Krypton]].
* MoralEventHorizon: Reactron crosses it in his first appearance, when he kills Supergirl's father while threatening to sexually assault her. General Lane does it when he transforms his daughter Lucy into a superweapon.
* TheyWastedAPerfectlyGoodPlot: Superman having a living Krypton nearby the Earth certainly poses certain storytelling difficulties but given they were an isolationist Utopian people, there was nothing preventing them from just being left alone unless authors had a plot for them. In short, an interesting element of the Superman mythos which could bring something NEW to the setting was destroyed because, "Why not?"