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: Chrono Cross
Alternate Character Interpretation: One fan theory speculates that FATE deliberately engineered the enmity between herself and your party via Lynx and his actions in order to motivate you to destroy her, both to free the Dragon Gods so they and the Time Devourer could be slain and to allow humans to make their own destinies, since she had realized she could no longer control or protect them from themselves. While unlikely, it does have a tantalizing resonance with Schala's Lavos-corrupted statement that she "love[s] you so much, I mustdestroy you!"
Anti-Climax Boss: By the time you get to the Time Devourer, chances are your party will be strong enough that attempting to defeat it through regular means will be a cinch; the boss preceding it is far more challenging. Of course, you'll have to do things a little bit differently to get the good ending...
Of particular note would have to be "The Wind, Stars, and Waves", more commonly known as Nikki's Concert, which is an in-universe example, as well as real-life Awesome Music. This link is a Let's Play video of the scene if you'd like the story as well as the music.
Ass Pull: Lavos being involved in everything. Even with the mention of Chrono Trigger's events, this comes out of nowhere.
Even more of an Ass Pull when you considered that two separate ports of Chrono Trigger had to involve massive plot recons to try and make this plot revelation work. Even then Lavos' sudden evolution to an unkillable god makes no sense and comes completely out of nowhere at the end of the game.
Base Breaker: Barring the game's music, everything. The battle system is generally thought of as fun and unique or needlessly complicated, and the story you will either think is deep and well thought out, or nonsensical, slow, and full of pretentious Broken Aesops.
8.8: EGM's Greg Sewart gave this game a 9.5 in a review that scored two 10s (out of three reviewers), denying it a Platinum Award (if the game receives a perfect 10 from all reviewers). To this day, Sewart receives hate mail from the fans.
Epileptic Trees: There's a theory running around the Chrono Cross fansites that Miguel's actually Crono.
Ending Fatigue: Disc Two, where each boss feels like the final boss, but inexplicably is followed by another one.
Ensemble Darkhorse: Guile, given the theory that he is an amnesiac Magus as implied in the secret ending of Chrono Trigger DS. He is more popular than most of the optional characters.
As far as other playable characters go, Leena, Glenn, and Riddel tend to be the ones who get the most fanart when you don't count the obvious Serge, Kid, and Lynx.
Foe Yay: Buckets of it between Lynx and Serge—even considering the fact he has a good In-Universe justification for it (Serge being the Chosen One), Lynx's desire to swap bodies coupled with a good deal of his dialogue is often disturbing and uncomfortable. Made worse when you find out he's Serge'sfather—although a good case could be made he isn't even him any more, between being combined with a panther and FATE's transformation/mind-wiping; other than one or two veiled hints it isn't clear if he remembers their relationship at all. Also, Harle, who flirts constantly with you both pre- ("So you are Serge! You are even more sexy zen I thought!") and post-Grand Theft Me ("Would you choose to save the world or me?").
A more Boring, but Practical Game Breaker is filling the entire first level of your characters' element grid with cure spells. That way, a quick heal is never more than a single high-accuracy-low-energy melee attack away, and you should almost always be able to max out your HP with your spare element levels after a battle.
Goddamned Bats: Beeba. Just as there are plenty of different mobs around, the turn system the game's based on makes fighting fast enemies very, very annoying.
"Leave it to Beeba! Beeba call friend!"
Schoolmates, with their high agility.
Hollywood Pudgy: The game has some pretty disturbing and unhealthy weight ranges for its characters. For instance, Janice's in-game body type is Plump, but really though, she's simply curvaceous.
She's listed at 5'7" and 104 pounds. Normal weight for a woman that height would be around 135 pounds or more; 104 pounds is freakishly thin. And she's not the only one. Miki is 6'0" and 115 pounds. That's the same height as Christian Bale and six pounds lighter than he was in The Machinist. More info can be found here.
Hype Backlash: Imagine, if you will, how much less Internet hate would be directed at this game if it hadn't been billed as a direct sequel to Chrono Trigger.
In Name Only: Cross is indeed a sequel to Trigger, taking place in the same universe, but it's just so far removed from its predecessor that some consider it this.
It's Easy, so It Sucks: Cross is only a little harder than Trigger. A lot of it comes from Serge, who is both overpowered and can't be removed from the party until New Game+.
Moral Event Horizon: The Dwarves lose every shred of sympathy they may have garnered once they massacre the fairies on Water Dragon Island. Furthermore, their use of smog-spewing tanks shows that they're Not So Different from the humans that they hate and aren't nearly as harmonious with nature as they like to claim.
Nightmare Fuel: Guile's first tech, Wanda In, which teleports his magic wand inside his enemy's innards and pulls it back out.
In-game: Throughout the game, Serge has flashbacks of the demon panther that attacked him as a child.
Lynx can be a pretty intimidating villain. When he first appears in the game, he mentions that you "saved [him] the trouble of finding you"; that means he's been looking for you, and you have no idea why. This is probably even more terrifying for Serge, since Lynx is literally a walking nightmare to him. Then there's the scene in Fort Dragonia where Serge and Lynx switch bodies; they both end up crying in pain because of this. Even after this event, Lynx in Serge's body is able to drag Serge's name through the mud almost instantly. And that's not even going into when Lynx transforms into FATE...And even though the revelation that Lynx is Serge's dad comes really late into the game, it still delivers a lot of Fridge Horror in the end.
Also, when Lynx as Serge first talks. The fact that Serge never really said anything up to this point makes it creepy. Then his profile image◊ turns to this.◊ Nobody's safe.
The FMV where the dragons become the "Time Devourer" has the Green Dragon suddenly making this face◊ and biting the Sky Dragon.
Player Punch: For fans of the original Chrono Trigger, FATE deleting Robo will have them screaming at the screen in tears.
Ditto the orphanage scene.
The Scrappy: Korcha, partly because he's such a good devil's advocate, and because he wears speedos.
To some of the detractors, most of the unnecessary characters. Like about thirty-five of them.
The dwarves. They appear to have been written to have sympathetic qualities, but their extreme bigotry, rampant hypocrisy (which the game NEVER acknowledges), and the outright murder of the fairies at their hands affords them absolutely no love. It doesn't help that if the player decides to bring Razzly along the second time they're met (which considering her involvement in the area the player is likely to do) causes them to get off scot free for what they've done.
Scrappy Mechanic: The element grid to haters of the game, since the player is forced to rely on it to get through the game. They will criticize it as making the game's battle system needlessly complicated, not helped by the fact that game has multiple tutorials to explain it which the player can NOT skip.
Strangled by the Red String: Serge and Kid. While they were obviously meant to be shipped together, given Radical Dreamers, and the relationship itself was established over time, there is a slight problem: you're never actually required to let Kid into your party, and even if you do, she's absent for much of the game. Yet you're still supposed to see Kid and Serge as a true love that stands the test of time, while poor Leena gets to be the Unlucky Childhood Friend.
Polis Police deserves a mention. The second boss you fight in disc 2 at the entrance of Chronopolis. It's physical attack is something that you need to be careful, but the problem is it's second form where he starts using Bazooka, a tech that guarantees one hit kill, even with White innate characters. That is unless you know how to use Diminish.
High Tier: Serge is so much stronger than any other character in the game that he borders on this. And you can't remove him from the party until New Game+ either. Glenn is also incredibly strong, especially with it's dual tech X-Strike with Serge. The only problem Glenn has is that you have to refuse to save Kid. And yes, if you don't do that he's Lost Forever.
Low Tier: Some characters, while not bad, get overshadowed by a better one. For example, there's nothing wrong with Orcha per se, but Zappa has mostly better stats, unique weapons, and actual plot relevance, which leaves Orcha on permanent bench-warming duty with Zappa around. And some characters like Sneff, Skelly, and NeoFio are just plain horrible.
Dwarf king: Is there no land on this planet where we can live in peace? Oh, Goddess of Fate, why are we dealt such a hand...
Kid: Yer mob literally just commit ethnic cleansin'. You seriously ain't trying to act sympathetic are ya? I just recovered from me death bed. I really don't wanna get sent back for my eyes rollin' outta my head.
Dwarf king: Are humans really the greatest species on this planet? These heretics of evolution, these destroyers of the planet?... Ugh...
Kid: Seriously, pal. You were just smashin' about with a soddin' smog spewing tank. I don't think that thin' popped outta damn turnip patch.
Dwarf king: Silence human. We are the ones dying! It is entirely your fault for having driven us out of our incredibly toxic swamp that was only being held together by a load-bearing monster from turning into an uninhabitable quagmire! Don't you see? You greedy humans and your wrecking of the environment caused us to mercilessly butcher another peaceful race so we could move into their much more vibrant and hospitable land to turn it into our new industrial stronghold. You monsters! Hi-ho!
Serge: Seriously, you're as sympathetic as the shit I took this morning. Have fun hi-hoing in hell.
Woolseyism: Not by Ted Woolsey, but it was translated in a way he would have done it.
Including retaining all the Woolseyized terms and names from Chrono Trigger — notable since the game was released around the time Squaresoft's US localization teams had begun to adopt a universal (and new) naming scheme for common elements (items, spells, etc.) in the Final Fantasy series.
For the English script, the localization team built in an on-the-fly accent generator that adds several dialects and accents for generic text and gives them to different characters. And they decided to put Kid in an australian accent...