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.
Alternative Character Interpretation: Did Magus's origins shape his villainous character in the middle ages? Or was he deliberately using a Machiavellian method to obtain power and defeat Lavos? Either way, it was rather selfish.
Magus is clearly written to cultivate this. The kid really had no chance: saddled with a chilly, uncaring mother and ripped away from his only supports in the world, Alfador and Schala, then raised by orcs in a pre-industrial dustbowl. On the other hand, he is a major war criminal and does pretty horrible things, besides; even when cornered on the cape, he chortles over Crono's demise and harbors no remorse for the dirty dealings he performed to get close to Lavos. The player can opt to kill him and lose no sleep over it, readily. On the other hand if the player doesn't kill him and lets him join the party his motives are still unclear; Is he joining them out of some regret for what he's done seeing their reaction to Crono's death? Is he only using them as a means to further his steps to revenge against Lavos? Is he using them but in fact as a way to find Schala? Some combination of those?
Lavos's true nature lends itself to a lot of interpretation and discussion. Is it merely an animal acting out of survival instinct? Is it a cold alien intelligence with sinister plans for Earth? Is it an automated world-killing bio-machine fulfilling some ancient programming? Is it simply a being with thoughts so alien humans can't comprehend them?
Ozzie barely qualifies as a boss, but in your first battle against him, he hides behind an impenetrable barrier until you hit a switch to drop him in a pit. In the rematch, while the first round ends with you dumped through the floor before you can do anything, a cat wanders in during the second attempt at the battle and hits the switch to dump him for good.
The Golemboss (Golem Overlord in the DS release), fought on the wing of a giant airship. Being afraid of heights, it doesn't attack you and runs away after a couple of turns. Killing it gives some nice tech points and exp though, if you're fast enough.
Badass Decay: Ozzie isn't especially intimidating even when you first meet him, but late in the game he's downright pathetic. In fact, the one time you actually fight Ozzie, he's accompanied by Slash and Flea, each of whom you've fought twice before, both times three-on-one.
And even saying that you "fight" Ozzie is a bit of a stretch there, as once you take out his two goons, he literally sits there and does nothing for the rest of the battle, simply letting you beat on him until the battle ends.
Best Level Ever: Magus' Castle and the Ocean Palace, don't you dare deny it.
Breather Level: The Prehistoric Era in general can be considered this, at least until you enter Azala's lair. Both times you visit, it specifically comes after the Wham Episodes like Crono's trial, an After the End future, and the war in the Middle Ages.
Fan-Preferred Couple: Despite Crono/Marle being the Official Couple (on top of being quite popular on its own right), a considerable portion of the fandom ships Crono/Schala. There's also Crono/Lucca for those who feel bad for Lucca. Magus/Lucca and Magus/Marle are also quite popular. And let's not forget Frog/Lucca.
Marle's Haste spell, and auto-haste equipment like the Haste Helm.
Give Crono the Rainbow (70% crit rate) and Fury Band (80% counter rate). Factor in that he can counter things like barrier changes and enemy revives and he becomes a killing machine.
Ayla by herself. She's got the highest Strength and Speed in the game (making her the party's best tank), can Charm exclusive equipment from bosses, is cheap to outfit (she doesn't require a weapon), and employs a variety of very effective low-cost Double healing techs with other characters like Frog. The only downsides are her lack of elemental attacks and pretty boring lines. The same can be said of her avatar in Chrono Cross, Fargo (and later Kid, when she finally rejoins): a good all-purpose fighter, but damned if it isn't tedious constantly seeing him in your party!
Also Dino tail.
Gold Studs! Get three Gold Studs to cut your MP costs, and you can spam your most powerful magic without a care in the world. This is incredibly easy to do as well as one enemy (Scouter in the SNES version, Flyclops in PS1) in the game gives them after they are Charmed. Combine this with Marle's Haste above, and you'll have a team that can spam Triple Techs like there's no tomorrow. Most bosses go down like chumps.
The Prism Spectacles dramatically increase the damage a character does. And we mean dramatically. Put them on your best physical hitters, like Crono with his 70% sword or his shiny new 90% crit sword, or just on Ayla, and their attack commands start hitting as hard as other characters' spells. Then, if you start casting with them...
The DS version gives Robo an arm with a base power of zero...but a critical hit is guaranteed to deal 9999 damage. Then equip him with the Dragon's Tear, which greatly boosts the wearer's crit rate, and even the Bonus Boss becomes a pushover.
Falcon Strike (Ayla+Crono dual tech). Low cost, learned relatively early, and insanely powerful. The only drawback is that it only hits on a horizontal line, but it is amazing how many enemy groups considerately line themselves up (including Lavos' final form).
Most final weapons from the DS remake. Lucca's can do more damage with a regular hit than Crono's critical hit if her current MP ends in 9. Marle's weapon does 777 damage on everything, which is decent damage to most enemies, but it even does that much to enemies with special defence - including bosses like Nizbel, the Black Tyro, and Lavos.
Goddamned Bats: Those rats and frogs from the Lost Sanctum bonus dungeon. You cannot avoid fighting them. Considering that the whole dungeon is one giant Fetch Quest Ad Nauseum, you will fight them well over 30 times just traveling back and forth. It's not that they're hard... but you just cannot avoid fighting them, so it breaks the flow and becomes annoying very fast.
Robo's theme sounds quite similar to "Never Gonna Give You Up." It's an odd feeling being Rickrolled in the middle of a video game. It's especially funny because when Yasunori Mitsuda was asked about it, he said he honestly hadn't heard of Rick Astley when he was composing the music for this game.
The oft-repeated joke about gear from as far back as prehistoric times being better/stronger than items made in the future takes on a new level when you think of planned obsolescence. It's entirely possible that civilization up to Lavos' attack subscribed to this theory.
Frog and Crono, to a lesser extent. The character that plays the Crono resurrection scene is determined by a priority list, presumably with the characters that are closer to Crono having a higher priority. Marle's first, Lucca's second. Guess who's third.
It's Short, so It Sucks : The most common criticism brought against this game. Though, even some of those critics admit that the tightly plotted story might make up for its shortness.
Its relative shortness works in its favour when you consider that the game has multiple endings; getting them all requires at least two playthroughs, possibly more if you're not leveled enough to defeat Lavos with just Crono and Marle at the start of the game.
Jerkass Woobie: Magus, thanks to a mixture of being incredibly badass but having one of the more tragic backstories in the game. The fact that he's an Ensemble Darkhorse doesn't hurt either.
Memetic Molester: Thanks to YTMND, the tune Burn Bobanga (the one that plays during a prehistoric party) has forever become associated with being molested.
Fail to save Lucca's mother from her accident. But if at first you don't succeed, try, try, again.
Fail to defeat Lavos...
The Ocean Palace Disaster, aka Crono's death, is approximately five Player Punches in a row. Magus fails, Crono dies, Schala disappears, Lavos awakens 14,000 years early and destroys Zeal, and then the Choose Your Party screen comes up without Crono in it, proving that, barring optional time travel shenanigans, he is indeed Killed Off for Real. Ouch.
Self-Fanservice: Magus is drawn in fan art as a typical White Hair, Black Heart type (that is, in addition to his long white hair, he is also drawn very pretty), but Akira Toriyama's original character design for him is anything but. Ironically however, later games in the series imply that, despite Toriyama's design, he really is quite attractive. To a lesser extent, some female characters like Lucca and Ayla.
In-game, Frog is only half of Chrono's height and artwork of him is almost always Ugly Cute. Not in fanart.
Magus, due to the constantly changing barriers, although thankfully he stops doing this midway throughout the battle. Depending on your party selection, he can be immune to your attacks up to half the time, and will likely always be immune at least one out of four.
Lavos qualifies, if you choose to face him at the very earliest possible moment in a New Game+ (via the Teleporter at the Millennial Fair). Since you're only going into battle against all three stages of Lavos with only Crono (and possibly Marle), it's arguably the game's hardest battle. But Lavos' defeat in this situation (or at said palace) is followed by the special "Developer's Room" ending.
The Lost Sanctum in the DS re-release. To wit: A series of blatant Fetch Quests involving inescapable, scripted battles, going up and down the same mountain at least seven times, and not being able to progress without speaking to the right NPC to set off an event flag, despite having all the items necessary to proceed. The rewards are quickly outclassed by those found in the post-game dungeon, the Dimensional Vortex.
Hell, most of the rewards are outclassed by those found in the sidequests that were in the original game! That said, the inevitable, scripted battles DO allow for a lot of Level Grinding and Tech Point grinding, so it is somewhat helpful.
This is ironic because fans have complained there was little to no connection to Chrono Cross since the early 2000s; now that there is, they're complaining about it, though that may be a statement on what those fans think about Chrono Cross (i. e., the fact that there was little to no connection to Chrono Cross was a point against that game and not Chrono Trigger).
Tier-Induced Scrappy: Marle is a particularly disputed one. She has the drawback of being a healer with no multi-target heals, and late in the game her offensive capability falls way behind everyone else's. Many players prefer to farm for Magic Tabs and pump Frog and/or Robo full of them so they have the magic power to heal effectively, and there's no corresponding way to raise Marle's offense. However, Marle has Haste and Life2, casts half of Antipode 3 (one of the best dual techs in the game), has tremendous natural magic defense and can wear the Prism Dress, which bumps her magical defense so high she can take a Dreamless/Dreamweaver to the face and keep smiling.
Done by Woolsey himself, no less! Likely the source of Ozzie/Slash/Flea being named as such rather than their original condiment-themed names. Also, Schala was originally named "Sara" in the Japanese version; Janus was named "Jackie." Similar to Tina/Terra, this is a case where the names that would've sounded "exotic" to Japanese speakers (but commonplace to English speakers) was changed to preserve the exoticism. Same goes for the Gurus' names, Gaspar, Melchior and Belthazar (which were "Gash", "Mash", and "Bash" in the Japanese version, but make a lot more sense in the English translation). See the trope entry for more.
In a subversion of using an "exotic" name, Woolsey changed Princess Mardia to Princess Nadia. Also, Janus' Japanese name is Jakki, not Jackie, though it's likely Woolsey didn't know that, either (both names are written the same in Japanese).