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.
Alternate Character Interpretation: The entire point of the series. Lex Luthor presents his side of the conflict between him and Superman. The point of the series is that, Lex's argument aside, he's a monster.
Additionally, do the final words "I am a man, I hope." mean that Lex thinks his hope makes him a man? Or do they mean that in the face of all the evil he has done Lex is clinging to hope that he is still a man? Both interpretations are valid.
The story has produced some differing interpretations over exactly how responsible Luthor was for everything that happened including the destruction of the jewelers/daycare center that drives the final act of the plot. Less responsibility would make Luthor a Well-Intentioned Extremist who perhaps tips over into Knight Templar territory, while more would make him a delusional mass-murdering lunatic. The story itself is somewhat ambiguous on several points, but suggests that the sheer depth of Luthor's Machiavellian personality makes it highly unlikely that he was completely unaware of what was going to happen even if he wasn't responsible.
Draco in Leather Pants: The fact that the story's understanding of (although it doesn't actually agree with) Luthor's worldview, coupled with some ambiguity over exactly how responsible he was for everything, has led to this being applied to Luthor from some quarters.
Misaimed Fandom: Luthor has persuaded some people — both in-universe and in real life — that Superman is a threat with his arguments. Also, that he's correct in his view that humanity must always fear aliens (by which he means this alien- Lex has always had less of a problem with actually malevolent aliens, like Brainiac, even teaming up with them at many points). The point of the story is that Lex Luthor, a human being, is about as big an enemy to humanity as humanly possible.
Moral Event Horizon: Lex's 'great contribution to humanity', his charity towards his janitor's son, and everything else — ends in tears. Lex still feels guilt, though — or, at least, he tells us he feels guilt.
Squick: This can be the reaction upon learning that Luthor essentially had sex with a robot, with further Squick possible upon realizing that Luthor's such a messed-up control freak that the only real relationship he can have is with a woman he completely designs and builds himself.