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: Knights Of The Crystal
Broken Base: The Ultimate Job System update; some hated it for removing the collections and making it take forever to power up jobs; others loved it for making jobs previously unavailable due to being promotions suddenly available again (particularly the Witch/Jack-o-Lantern) while improving what could be done with old jobs (Machinist, for example, went from improving quest drop rate from a maximum of 4% to a maximum of 14%).
Game Breaker: In general, the Onimusya class in the arena. While literally bottom at defense, they make up for it with such an absurd amount of attack that they break the Tactical Rock-Paper-Scissors of the game. They're really only beatable by Instant Death attacks, high-level Gold and Ultimate cards (if similarly unbalanced in stats), or another Onimusya getting a boost from a formation. The game later introduced the gold-level Shogun class, which was even worse, with more power and one of the aforementioned Instant Death attacks. Oh, and it gets a huge boost to its attack if in an arena formation with Onimusya and Samurai (mentioned above). Even with the power creep in the cards introduced since the Shogun, it remains an arena mainstay.
On the questing side of the game, the Cannoneer. Its arena abilities were underwhelming even when it was introduced (before further being eclipsed by So Last Season concerns), but its main ability was to reduce the AP cost of quests by a maximum of 5, minimum of 1. This breaks the experience curve, not to mention the Play Every Day and Anti-Poop Socking features in the game. A merge using the Cannoneer was likely introduced to encourage players to stop using them to break the game.
They Changed It, Now It Sucks: The new "Ultimate Job System" introduced as of March 8, 2011 is already getting some complaints, mostly because collections are no longer needed to get classes, but only objects, and classes became job cards which are far more underpowered and need a long, time-consuming process to get improved.