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.
The fact that the names are so awesome McCool can be chalked up to the fact that it's an RPG. Think about some of the names you give your RPG characters.
The infamous plot twist also neatly explains the frequency of human aliens in the setting. The designers of the Eternal Sphere would want their players to be able to relate to and connect with their characters. For most players, that means a character that looks mostly human.
Game Breaker: It's an art for so many players to find the fastest and most efficient ways to remove any challenge from the games. In Till the End of Time, for example, doing so will almost certainly involve either Orichalcum or the Boots of Prowess, depending on where you are in the game.
The Scrappy: Both of Nel's subordinates: Tynave and Farleen. Their English voices make it worse. Tynave's voice is perfectly fine, but listening to Farleen would have you swear that the air of Elicoor II was full of helium.
Adray is considered by many to be an unnecessary addition to the Director's Cut/overseas versions. This is due to him being (barely) shoehorned into the plot and is forced into your party, which prevents you from recruiting all of the characters that you want. His subpar and overall awkward combat performance also earns him a lot of hate. The fact that he joins you instead of the actually important fan favorite Clair only makes things worse.
Shocking Swerve: If you've played it, or even read a few spoilers, you'll know.
They Changed It, Now It Sucks: Many fans of the series, especially of The Second Story, hate Till the End of Time for the changes it made to the item creation system and other aspects, besides the infamous plot twist. To be fair, most of the hate is not due to the fact that it was changed, but due to the new systems being unwieldy, overly dependent on randomness, insanely expensive, and very frustrating.
They Wasted a Perfectly Good Plot: The infamous plot twist was wasted; it might have fared much better if it was used for something else. Such as having an ally turn out to be a player character mole or examining the impact common MMORPG behavior would actually have on its universe.