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.
Alternative Character Interpretation: It's deliberately left ambiguous if the Overmind is just in its manipulation and eventual assimilation of sentient races. The Overlords believe that it's a good thing, but they're basically the Overmind's slaves.
Esoteric Happy Ending: The Overlords think it's a happy ending, and the idea is that the children of the last generation of humans Ascend to a Higher Plane of Existence, but it also involves the extinction of humans as a species, and the children are incredibly creepy. Not to mention the fact that the Overmind has done this possibly hundreds of sentient races. If a different science fiction work kept the same basic plot and cast the aliens as villains, most people wouldn't bat an eye.
Never Live It Down: In-verse. The leader of the island community admits that as a Jew, he never really got over his faith being discredited or his old homeland (Israel) giving up its independence so soon after it attained it thanks to the Overlords. Still, he doesn't have any particular grudge against them.
Older Than They Think: Clarke joked in his updated prologue that new readers will think that the opening scene with the fleet of alien ships blocking the sun was ripped off from Independence Day (despite this being written in 1953!). In fact, Clarke himself knew of an even earlier story with the same scene.
— Arthur C. Clarke, in the Sources and Acknowledgments section of 3001
Uncanny Valley: The faces of the new generation, which resembles the type of 'average face' created by compositing many photos together and is even more expressionless than a corpse.
Values Dissonance: The book was written when feminism was in its early stages, so there are a few jarringly sexist things with the men running the show and Jean only acclimating to New Athens when she learns to appreciate the kitchen.
It also attempts to challenge racism through making "nigger" a polite description no more taboo than "republican".