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.
Designated Villain: All Dandelion and Savory wanted was justice for Chickory's death and for society to stop being so apathetic, corrupt and reliant on technology. If it weren't for the bombing, they'd be little more than a more organized and successful version of the Killer Elephants.
Esoteric Happy Ending: The good ending has the villain and his right hand killed and his plot to destroy society thwarted by the protagonist's actions. The bad ending has the protagonist take over the villain's plot and successfully execute it himself. The former is by far the more depressing of the two.
There's a trick, about halfway through the game when you get to Happy Garland, where you can bet on one particular arena matchup and use some basic luck manipulation to win every time, raking in obscene amounts of money for your trouble. To whit; Samson will beat Saffron fully 2/3rds of the time, even though he has far worse odds, provided you sit and watch the match (as opposed to skipping it and allowing the game to calculate the outcome based on odds). The game becomes much easier when you can afford to buy multiple copies of everything in the game.
The wall bounce glitch, which involves hoisting an enemy over your head, then tossing them against a wall and standing between them and the ground, essentially juggling them off your head and KOing them in a matter of seconds. This is actually quite useful if you don't want to try and spend time on earning powerful parts and developing strategy.
Fossil excavation can get you hundreds, possibly thousands of dollars to buy whatever weapons you want near the beginning of the game. All you need is a flatbed, and you can mine fossils right outside of Nefroburg and sell them to the museum.
Moral Event Horizon: The leader of the Bloody Mantis Dandelion, crosses it when he orders the Bloody Mantis to bomb Happy Garland into the stone age to get revenge on technology. If you join up with the Bloody Mantis this can become your Moral Event Horizon too.
Narm/Narm Charm: Some players believe the songs fall under one or the other. The main point of contention seems to be the lyrics, with certain verses sounding either cheesy or awkward in grammatical structure as if the lyricist was not a native English speaker. A rumor amongst the fan base is that Fennel's song in particular attempted to invoke this.
Player Punch: Quite a few, actually. There's the artist Pablo, and in the hero ending when Savory jumps in the way of a shot meant for Dandelion. The second case is made even more sad as it seemingly leaves Basil in a depression so severe that he's found living under a bridge in the year after mode.
The entire game could have been a deconstruction of the amnesiatic hero cliche, and the game already did in some ways by allowing players to choose Vanilla's history at one point, not to mention avoiding having him be a powerful warrior all along.
The two worst offenders would have to be the leadership roles of the Killer Elephants and the Bloody Mantis. If you assume command of the KE, that's it. No raid missions, no optional tag-along bodyguards, not even a resolution to the former leader's desire to travel to the moon! And the latter is even worse as you get thrown in jail immediately after the credits and never get to do ANYTHING with your new army.
The romance angle also suffers in some way. While it is possible to play the game and have Vanilla essentially be in love with Connie (and hints of her feeling the same), the game never allows you to take it any further than the two simply sticking together in the year after mode. Come on, where's the romantic embrace and kiss?
The Woobie: Basil can be seen as such as his unrequited love for Savory is continually ignored. There's even an option to convince him Vanilla got "personal" with her. When Savory turns evil and dies, Basil has a mental breakdown that he never recovers from.