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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.
There are those who solely enjoy the manga but dislike how Tsubasa Reservoir Chronicle intertwined with the plot particularly with Yuuko's and Watanuki's pasts. And in order to understand it, they have read the other manga but still it made things more confusing.
The manga's ending divided people. Some people believe that the series should have ended with Volume 16 as the last chapters did not build up anything to the story. CLAMP themselves acknowledged people's reaction to the ending and were happy since some wondered about Watanuki's fate.
xxxHOLiC: Rei also divided the base. Despite that Yuuko is back, some people still find it more of a rehash of the earlier volumes without any new input on the story. Then, it went into a hiatus just to make room for Tsubasa World Chronicle which anger several readers. And despite that the two mangas are still connected, some readers felt that Watanuki and rest would only get some cameo appearances.
Shamisen/Plectrum. Which technically isn't a cargo ship since it's actually cat/butterfly. Maybe. It gets confusing when their human forms look like their owners. And it only gets more confusing when you realize that the bit of the plectrum's form we get to see looks very much like a certain deadexorcist.
The only universally accepted pairing within the CLAMP fandom is apparently Larg/sake.
"Funny Aneurysm" Moment: All Watanuki's wailing in earlier chapters about how his service at the shop kept getting prolonged and was NEVER GOING TO END? Yeeaah.
To be fair, the reason he isn't popular with girls probably has more to do with his flailing and screaming at things no one else can see than his looks.
Ho Yay: Once again, it's CLAMP. There's subtext not only between Doumeki and Watanuki, but also between Watanuki and Haruka, who he is much more willing to admit fondness for.
Subtext between Doumeki and Watanuki?! Subtext?!! CLAMP is certainly pushing "subtext" to its limit - hell, recent chapters have Doumeki and Watanuki alone in a bedroom, with Watanuki wearing a loose kimono, discussing about the mating habits of cats, and what it needs for the ideal mate and love.
Although you can consider the "longing for" and sideways glances in reference to Watanuki's constant longing for Yuuko. Doumeki's proven he doesn't approve of Watanuki's choice, after all. He never does.
Judging by the hints given in Rou ten years or so have gone by, Himawari is married and only visits the store once a year, while Doumeki and Watanuki spend almost every afternoon together. Doumeki goes out to work, brings the groceries, Watanuki cooks and serves the food, then they talk about anything while watanuki bends around the floor with his clothes almost falling off. Their relationship seems to have almost completely become that of a married couple if it weren't for Watanuki somehow managing to remain rather frustratingly ambivalent.
The latest chapters have become increasingly homoerotic, such as when after granting a ghost woman the wish of being reunited with her long lost lover, Watanuki recieved an umbrella as payement and; while explaining to Doumeki that finding a beautiful woman under an umbrella is an amazing discovery for any man, he walks femininely under said object and winks at his friend. Whether this is CLAMP's subtle way of messing with our minds or something more remains to be seen, and most probably never will.
On the opposite end, Yuuko is a wee bit touchy-feely with one of the early clients, as well as the twins in one of the earliest chapters (even kissing one of them.)
I Knew It: A large number of fanfics had predicted that Watanuki would inherit the shop and sure enough...
Late-Arrival Spoiler: Apparently, thanks to the anime adaptations of Kobato and Blood-C, everybody, including those who don't read the manga, know that Watanuki will inherit the shop from Yuuko.
Moral Event Horizon: If hurling a cup of boiling hot water at Watanuki for daring to befriend Kohane doesn't turn her mother into an irredeemable bitch in the eyes of the reader, then hitting Kohane on national TV should do the trick.
Pair the Spares: Despite the copious amounts of Ship Teasing between Watanuki and Doumeki as described above, the last two chapters would reveal that Doumeki eventually had offspring with someone else, as the Doumeki Watanuki's interacting with is not Shizuka Doumeki, but rather his great-grandson. To the shock and confusion of many fans, it turns out Doumeki married Kohane, who not only didn't have much significant interaction with Doumeki, but also was in love with Watanuki.
Granted, it should be noted that Doumeki appeared to have a soft spot for Kohane, and she is also the one who Doumeki confided in the reason as to why he chooses to stick around Watanuki. It can also be inferred that they began to interact more with each other off-screen, as it was stated that Kohane came to study under Doumeki at the University in the same field as him. It's highly possible that when the reality set in that Watanuki would be trapped unaging at the shop far longer than either of the two would be alive, they chose to get together for the sake of leaving behind descendants who'd stay by Watanuki's side.
Paranoia Fuel: The new series xxxHolic Rei is responsible for this. The choice of setting including Yuko alive and Watanuki as his assistant even though the original the series ended with Yuko dead and Watanuki as the shop's owner is leading many people believe that the entire series is about Watanuki escaping from reality. Latest chapters appear to hint this as Yuko and Domeki, and later even Himawari are shown to be aware of Watanuki having to make an important decision while in chapter 23 Watanuki even talked like his xxxHolic Ro persona much to his and the readers' confusion.
As of the latest chapters it's been revealed that Watanuki's subconscious, in the process of gathering some things for Syaoran from another dimension, had accidentally created the setting to emulate the time in his life when he was happiest, and that out of concern for his wellbeing, Himawari and Doumeki decided to follow and watch over him. Yuko on the other hand is stated to be a projection created by him, although it seems that she in of herself developed an identical will to the "true" Yuko.
Ship Tease: As mentioned in Ho Yay it's Clamp. Watanuki and Doumeki have a lot of tension between each other.
Interestingly this troper noted before the manga ended that Clamp was also hitting Doumeki X Kohane but in a more subtle way. We have Watanuki in volume 18 making a grin when Kohane calls Doumeki by his first name. Watanuki calls Doumeki stubborn when wondering why both are studying folklore in the same university which Doumeki dodges. In the same volume, a customer claims Doumeki was dating somebody but it might be a misunderstanding. However, the Ova made it canon.
Uncanny Valley: Occasionally the TV animation (and especially the movie) slips into this. One reader of Anime Insider wrote in after they featured Yuuko on the cover and asked, "Why did you put a sexy zombie on the cover?" (referring to this image) and managed to just about sum up most people's grievances with the art in one sentence, while simultaneously spoiling a major plot point unintentionally.
The Woobie: Jesus hell, damn near every major character is a woobie in some form or another, Watanuki, Kohane and Himawari being the most prominent examples.