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.
Darkness-Induced Audience Apathy: Not so much at first, but later series such as Ultimatum caused this reaction. Additionally, the fact that many of the characters became jerkasses via adaptation put quite a few people off. Killing off Peter Parker, the only nice super-hero this universe had, was the last straw for a number of readers.
The Ultimate Jessica Drew became a pretty big one.
Fanon Discontinuity: Pretty much everyone likes to pretend that Ultimates 3 and Ultimatum never happened.
Hilarious in Hindsight: When the Ultimate Universe was first started there were some rumblings and rumors amongst fans that Marvel was going to use it to reboot/replace the mainstream universe (which obviously never happened). Years later this ended up basically happening over at DC.
They Just Didn't Care: When Jeph Loeb started writing for Ultimate Marvel, fans noticed some odd continuity errors cropping up. The Wasp, an Asian in the Ultimate Universe, suddenly turned white like her mainstream counterpart. Meanwhile, Ultimate Pyro, who was a hero instead of a villain like the 616 universe's Pyro, and the duo of Forge and Longshot, heroes in the standard universe but villains in Ultimate Marvel, suddenly switched sides with nary a Hand Wave as to why. Pyro even wanted to rape a knocked-out superheroine, and lost the horrible scars that had been his most striking feature in Ultimate X-Men. Nobody knows exactly what went through Loeb's head, of course, but the most popular explanation is also the simplest - he didn't bother reading their appearances in other books before he wrote his own. The Ultimate Universe in general is plagued by this trope, apparently being seen as the branch of Marvel where continuity doesn't matter. One of the first Ultimate books was Ultimate Marvel Team-Up, which ostensibly existed to create Ultimate versions of characters who didn't have their own books. Unfortunately, those versions were roundly ignored as soon as someone felt like using those characters in a different book. They included Ultimate versions of the Hulk, the Black Widow, and the Fantastic Four that bore far more resemblance to their 616 counterparts than to what would later become the canon Ultimate versions.
Seasonal Rot: Ultimates Volume 3 and Ultimatum are both considered horrible, and the start of the rot period, and most definitely the height of it. It's easy to see why Marvel relaunched the line as Ultimate Comics afterwards. Ultimate Spider-Man is usually exempt from this, though, and hasn't ever really had been hit with the trope, with the worst of it being volume 3's Broken Base regarding Miles Morales.
Win Back the Crowd: After the utterly atrocious Ultimates Volume 3 and Ultimatum, the new line of Ultimate Comics are clearly trying to do this. It's debatable how successful this was, but it's generally agreed that the books have gotten better now that Jeph Loeb is nowhere near them.