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.
YMMV: The 39 Clues
Alternative Character Interpretation: Is Alistair Oh an old man who genuinely cares for Amy and Dan and feels regret for leaving them for dead time and time again and being there when Isabel set the fire that killed their parents, or a backstabbing enemy who feels no remorse for his betrayals?
Ian Kabra tends to be subject to this for several reasons, but since his going rogue in The Dead of Night, the question of his true nature is definitely up for debate. However, it turns out that his departure had nothing to do with any form of betrayal (except his mother's) and that The Mole was actually Sinead Starling.
Broken Base: The trading cards and website, especially the cards. Why? In the opinion of many fans, the pictures of the characters on the trading cards do not live up to the characters' descriptions in the books or the way that readers imagined the characters to look like, or else simply do not look appealing (a common complaint is that Ian and Evan look too much like Justin Bieber). The rest of the fans either like the pictures on the trading cards, or just like the trading cards and couldn't care less about what the pictures look like.
When the official message boards were made canon in The Dead of Night, some fans blew a gasket. Others eagerly played along with Evan's posts on the message boards. It's hard to find someone without a clearly defined opinion on this development...
It is difficult to find a fan who does not believe that the infamousKurt, who briefly appeared in one book and was never seen again, was an undercover Vesper.
A friend of Amy and Dan's Uncle Shep was mentioned once in the first series. But due to his name (Gregory Tolliver) and the revelation that Arthur Trent, Amy and Dan's father and Shep's cousin, was a Vesper, people not only believe that this friend is probably a Vesper, but that Evan Tolliver is related to Vespers as well (if not a full-blown undercover agent). This fandom sure does love its Epileptic Trees...
Since the revelation of Isabel Kabra's maiden name (Vesper-Hollingsworth) and of the fact that Arthur Trent is a Vesper, a great deal of fanon involving them has sprung up. It's taken for granted that they interacted with each other when younger, and many fans believe that they were romantically involved, though there is no canon basis for this. (Although the fact that Isabel knew about the "moon face" thing that Arthur and Dan used to do, enough to use it to manipulate Dan with the "AJT" texts, may imply that they were close.)
Quite a few fans are absolutely convinced that Amy's full name is Amy Hope Cahill, seeing as her brother's full name is Daniel Arthur Cahill.
It's generally accepted that Amy and Dan got their green eyes from their mother, and although Canon gives no evidence supporting this theory.
Foe Yay: Seeing as most of the main characters are adolescents caught up in centuries-old feuds, this is eveywhere. Mostly between Amy and Ian, especially in the third book, but it can be seen between other clue hunters, too.
I thought Foe Yay was supposed to be subtext. Amy and Ian are practically the Official Couple... at least in the first series.
Fridge Brilliance: In the first series, Amy and Dan were often shown to have sibling telepathy, but that has all but disappeared in the Sequel Series. It is because, as Dan grows darker and more emotionally distant from his sister, he and Amy can't understand each other as well as they used to.
"Funny Aneurysm" Moment: Ian's famous "Shoot to kill?" line in The Medusa Plot is suddenly not so funny anymore after Evan is actually shot and killed at the end of the Sequel Series. After he and Ian seemed to have been starting to develop a friendship, no less.
God-Mode Sue: What you will become if you drink the master serum.
And Isabel did.
Harsher in Hindsight: The ending of The Sword Thief, where Alistair fakes his death to escape and later in the first series, when he pretends to die of heart failure to trick his Evil Uncle, are not nearly as amusing after reading Trust No One, where he is Killed Off for Real as a result of a seizure.
Ian's thoughts when his sister is kidnapped aren't exactly uplifting to begin with, but they become even more painful after she dies, along with their estranged mother.
"It was funny... [Ian] didn't even like Natalie. But now that Mum had disowned them and Father was out of the picture, Natalie was his whole family."
And by the end of the Cahills vs. Vespers series, Ian has it even worse than before. His sister, the only person he really had left, is killed in Day of Doom. Their mother, Isabel, finally shows a shred of humanity upon learning of Natalie's death—but in her rage, she drinks the master serum and ends up dead, as well (though not without a glorious Dying Moment of Awesome). His father is still in hiding and seems to want nothing to do with him. And that's probably just the tip of the iceberg, considering all the issues that being raised by Isabel left him with, as well as the fact that not everyone in the Cahill family completely trusts him yet.
Romantic Plot Tumor: In Day of Doom, especially with the by now infamous Amy and Jake Love Confession in the closet scene. Even many of the pairings' supporters found its portrayal in that book to be cheesy, OOC, and ill-timed.
Ron the Death Eater: Quite frequently for Evan Tolliver and Kurt. The most commonly found demonization is making them turn out to be undercover Vespers, but fanfiction involving Evan suddenly dumping Amy is also becoming common.
Luke Cahill is sometimes treated this way, for no apparent reason other than he liked to sneak around more than his siblings. He did also become somewhat of a Jerk Ass in his later years, but he was never evil.