Alternative Character Interpretation: House Cannith: The world’s best war profiteers or a bunch of raving lunatic scientists doing what they do to just to push SCIENCE forward. (Since Cannith is split into three rival factions, it's quite possible for them to be both and more.)
The setting was designed to be ambiguous in regards to major events as well as factions and people, so that DMs could choose their own interpretation.
A lot of fans, at least in modern circles, have taken King Boranel of Breland, a heroic adventurer-king and one of the few well-established Big Goods of the setting, and turned him into a meme-parody of Teddy Roosevelt complete with "Borry Tigers" as a parody of Teddy Bears.
According to the handbooks (and themselves), the Undying are animated by positive energies, unlike normal undead, who are animated by negative energies. An alternate read would be that this is just propaganda; Undying are in fact not any different from normal undead.
Broken Base: Many "traditionalist" Dungeons & Dragons players found the setting too radically different from the earlier Medieval Fantasy/High Fantasy settings like Greyhawk, Dragonlance and Forgotten Realms. Ironically, the main complaint was that the setting was just too different from the already existing ones, which was kind of the point of launching a new campaign setting in the first place.
Complete Monster: "The Chimes of Midnight", "Quoth the Raven", "Hell's Heart": Genius Inquisitive Viktor/Victor Saint-Demain has his massive ego bruised by Baron D'Medani and plots a gruesome revenge, recruiting serial killers to commit murder all over Sharn with intention of wiping out the Baron, his House and to drop D'Medani's beloved daughter Zelina to her death. Foiled and placed in a sanitarium, Viktor manipulates a troubled man into becoming a serial killer who kidnaps and tortures his victims to death, with the intent of sending the heroes to die against him after creating a large body count. Locked away in the asylum of Hell's Heart, Viktor uses his manipulative brilliance to take over, allowing the insane doctor in charge to torture other inmates, before recruiting more serial killers. Having the D'Medanis captured, Viktor tries to have them killed, intending on framing the heroes for poisoning Sharn's water supply to kill thousands upon thousands of innocents, releasing his killers on the population and "clearing" his name to take advantage of the horrible chaos.
Fanon Discontinuity: While many of the changes for 4e stuck nicely, introducing Tieflings, Dragonborn, and Eladrin into Eberron, fans generally agree that there is not now nor has there ever been a 14th Plane called Baator! Upgraded to Canon Discontinuity as of 5e, as Eberron: Rising From the Last War doesn't mention it at all.
Ho Yay: Yaoi Genrefans might enjoy the fact that the kalashtar are described as having a strong preference for the company of members of the same quori lineage, and do not commonly form long-term relationships or marriages with members of other lineages. Since each lineage consists of only one gender...
It Was His Sled: King Kaius being a vampire is basically an Open Secret among the fandom. Eberron: Rising From the Last War even had open speculation about his true nature where the players could read precisely because it was already so well-known.
Nightmare Fuel: The Daelkyr are pretty horrifying to start with, being really powerful and completely alien creatures from Xoriat. It's even worse when you consider that they look almost exactly like humans, the implications of which are unclear, but the most likely reason is they created humans (and possibly all humanoids.)
Older Than They Think: There's plenty of new material in Eberron, but some ideas like Elemental Airships were already used in Mystara. Jakandor could also be seen as a proto-Eberron, with two morally grey factions that the Party could be members of, rather than the dozens of organizations, houses, nations, and religions vying for control of Khorvaire.
Once Original, Now Common: Some of the elements that originally helped make Eberron unique, like liberal use of Magitek and rejection of D&D's traditional Always Chaotic Evil approach to monsters, have ended up becoming a feature in a lot of other settings, to the point where younger fans might not realize how unusual (and as Broken Base above shows, controversial) those ideas were when Eberron was first published.
Vindicated by History: While Forgotten Realms remains the most popular D&D Setting (thanks to Wizard's contract with Ed Greenwood requiring at least one new Forgotten Realms book each year), Ravenloft is really the only other contender for the #2 slot. Beyond that, Keith Baker indicated that adapting Eberron to 5e was extremely easy because in the past decade D&D as a whole has drifted strongly toward the Dungeon Punk feel of Eberron, and now assumes Settings in which magic has mundane utility as the default, something for which Eberron was heavily criticized for upon its initial release.
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