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.
Big Lipped Alligator Moment: In the Desecrated Shrine, the gang suddenly come across an abandoned porn magazine that just happens to be there. Hilarity Ensues, and is never mentioned again. Not even when you find the Adult Mag Bonus Boss, which this was probably foreshadowing.
Complete Monster: Although Karitkeya initially appears to be an average Psycho for Hire, it's revealed later via flasbacks that he shot Greg's 5-year-old son and his wife for trying to protect Greg for no real reason other than it was a fun way to play with his new ARM. His reason for attacking Greg and then letting him live after murdering his family? Again, just for the fun of it.
Dean is a close second, as many fans find his unwavering optimism to mean that he's out of touch with reality...or that he's just plain dumb.
Surprisingly Improved Sequel: One of the best Wild Arms games by far, but notable is the improvement of the HEX-system. Rather than having to choose, all characters can both move and perform an action during their turn (In Wild ARMs 4, only Raquel could do this). Experience is also evened out and abundant. In addition, half of the characters don't have to be next to their targets to attack, with Rebecca and Greg being able to shoot anything in a straight line and Carol being able to shoot any HEX she wants.
That One Boss: Several, but the Four Sentinels are among the most difficult each having an attack that deals insane amount of damage being downright One-Hit Kill. The fact they have means to counter their own weaknesses also doesn't help either. And to make matters worse, you immediately have to fight them again as a Duel Boss.
They Wasted a Perfectly Good Plot: General consensus is that the ending is less interesting than it could have been on several accounts: explaining Avril's amnesia with "It was a Stable Time Loop" and Volsung's villainy with "He was possessed." Many were hoping for more intricate, complex answers to those questions, rather than explanations that can literally be summed up in one trope.