I can't make any arguments against the reasons this manga is considered creepy, but they also have almost no effect on my emotional reaction to it.I still like it, god help me.
Chobits is about a honey-eyed, cat-eared girl robot and her quest for love. After a memory loss, she starts out only able to say "Chi", and taken in by a broke-ass young Joe named Hideki Motosuwa, the main character. Chi has a tragic past, a mystery that gradually unfolds, and there is some meditation on the issues raised in a world when robots like her (actually nearly-human computers called "persocoms") can mimic humans so thoroughly. Hideki and Chi eventually fall in love, transcending all obstacles.
Yet let's get real: it's wish fulfilment. Though Chobits was made by women, Chi is also spank fodder, portrayed with a disturbing combination of innocence and sexual suggestion. Hideki initially has to take a paternal role to teach her memory-wiped self, and because he eventually falls in love with her, it's two times the creepy. Furthermore, though Chi has an inner life of her own, it's mostly brooding about her feelings for Hideki.
To underline the set-up, while male persocoms do exist and have adoring women on their arms, any "futuristic" couple in the named cast involves a female persocom and a male human, paving the way for Hideki and Chi. The "just for men" angle, though thankfully only implied, makes it even harder not to find the story unsettling.
And Chi, as it turns out, can't have sexual intercourse without being re-set, because her re-set button was deliberately put in her no-no place as a way to "test" how deeply a future lover could care for her. Hideki, despite his huge collection of porn and comical horniness, agrees to the condition and lives happily ever after with her.
When I was younger, I found the final reveal subversive and touching, since Hideki, though good-hearted, assumed Chi would perform sexual services when he first found her, and this was dialing back the wish fulfillment. Now it comes off as weird virginity/abstinence fetishism, as if a love can only be "pure" without sex.
However, the illusion of poignancy and substance is impossible to shake entirely, and on some levels I still believe in it, that Chobits is merely a heartfelt sci-fi love story with elements of a mystery, weirdly charming.
There's also the balls-to-the-wall assertion made at the end: even though no persocom has anything but programmed emotions, it doesn't matter as long as humans feel attached to them, and persocoms feel attached in turn. Somehow, Hideki can say "Chi's heart is real; it beats inside of me" and I'll want to believe it, despite the lack of substance in their relationship. That's such determined advocacy for simply wishing things to be right, it's almost admirable.
In the series, some female characters relate their bad experiences with persocoms, involving abandonment and jealousy, but this never creates any long-term consequences for the cast. This social analysis is eventually swept under the rug in favour of straightforwardly pursuing Chi and Hideki's romance.
Stories should not lecture to the audience, of course, nor need be politically correct to be good, but it's easy to see this dropping of conflict as a way for the story to create the illusion of deep consideration without confronting the issues it raises. If a moral conflict is introduced, a story should pursue it to the end, or at least explain why the conflict does not apply to the leads. Maybe the message is supposed to be that others' bad experiences can't spoil a valid concept?
The last part of the manga runs on this same kind of strong individualism, as promoting the complexity of love's form replaces the exploration of the dark side of persocom existence. Oh, and there's also a lot of creepy incest overtones, though none involve literal blood relations.
I've seen several people explain why Chobits is a cut above other male-fantasy manga, and maybe it is (I wouldn't know). The anime version is also worse, dragging out the sex comedy parts with filler before it reaches the heart of the story, and having a less coherent ending. Yet even with this in mind, Chobits is still shaped like itself. No amount of aborted conflict or earnest emotion can disguise the creepiness. At the same time, I can't let go of it. I let myself get bamboozled every time I read the series.