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.
Alexandra. She's quite an intriguing and complex character. There are way too many interpretations to list them here.
The Lord of Jewels. Was the Jumi arc a plan to save the Jumi race from extinction on his part?
And if so, did he realize that the main character was suffering emotionally enough from Sandra's genocide to form a crystal teardrop on their own, and would do so once he was defeated and the quest was over? To put it another way, was he aware that both outcomes of his boss battle were likely to save the Jumi?
Anticlimax Boss: Lord of Jewels 1000. You can't lose to this guy if you try. He barely even fights back. It's especially disappointing after Lord of Jewels 999, who was (by Legend of Mana standards at least) fairly difficult.
Due to the wonders of alchemy and weapon tempering, it's possible to beat the final boss in two hits. Of course, that's on normal difficulty settings.
Contested Sequel: This game did some things very, very well. It did some things very, very poorly. When you play it, you will either forgive the flaws, or you won't.
Crowning Moment Of Awesome: Cap'n Tusk insisting that Elle go ahead and sing. The voices of sirens cause nautical disasters. Tusk keeps his ship afloat anyway (with a little bit of monster-slaying help from you, of course).
In a way, Sandra ripping her own Core out and throwing it to the Lord of Jewels.
Demonic Spiders: Zombones. They have a long reach, no attack windup animation, and one of their attacks squashes your character flat and then s/he can't move until un-squashing. Well, Zombone can spam the squash attack and you can get killed without ever having had a chance to fight back. Oh, and you only get 3 exp crystals for killing one.
Ear Worm: "Blue Gloom", played partway through the Jumi storyline.
As Flameshe explains to Elle, being yourself is the most important thing, and whether other people get killed in the process doesn't matter. Furthermore, doing something for the sake of someone else because you don't want to hurt them is wrong.
This goes straight into Broken Aesop territory as the Player Character is looked upon to solve the very problems caused by others' passivity. (Possible Accidental Aesop: "It doesn't matter what you do, the Chosen One is going to breeze through and fix all of your problems", perhaps?)
A girl's friend is dying and has already given up hope. The advice of Gaeus the Wisdom? "She said to let her die, so let her die."
Game Breaker: Prodigious Gold Coin farming, combined with some smart Item Crafting, can net you your very own weapon that can slay gods even on No Future Mode. If you exploit the crafting system for all it's worth, the Infinity+1 Sword and Armor of Invincibility you can end up with make the game pathetically easy.
Also, using Blackpearl as your NPC assistant, as her synchronization effect instantly fills your Charge Meter.
a Robot Buddy Golem with a Infinity+1 Sword as a key ingredient in its Logic Block can wipe out average monsters with ease. this Troper remembers one time his Golem did this move where he shot a laser out of its ass and took a regular difficulty boss down by three health bars.
Some of the Mons, normally overlooked for the Golem, can be Game Breakers as well. The Synchro Effect for the Succubus pet is HP Drain. If you have your crafted Infinity+1 Sword, you can easily heal yourself to full in a single attack. Even nastier is the Synchro Effect of the Springball - Invincibility.
Goddamn Bats: Depending on your weapon equipped, any monster can either be a walkover or massively irritating, but high controller throwing points go to monsters that can confuse you (reverses your controls), drop your Charge Meter to zero, squash you, freeze you in place, or set you on fire.
Guide Dang It: EVERYTHING to do with crafting — the information you're given when you receive your crafting tools is so inadequate as to be laughable in the face of this kind of complexity.
Heres exactly how you create best weapon of one type in the game. You need to capture a Pet that have specific ability that is necesary to get the material you need. Then, you need to grind in specific place and bringing along said pet to get money to buy the ridiculously expensive material in ridiculous amount. Then, you need to grow a number of specific fruit, and farm certain item and coins for your weapon. Then, you need to grind for something that Randomly Drops for the weapon material, but the chance is ridiculously tiny. Finaly, you need to follow a set of Forge/Temper step that take hours to complete. Heck even after using guide, its still hard to understand the process. Imagine doing this all without a guide. That involve knowing where to farm, Understanding how the system work, and understanding the effect of each Material and their result and figuring the step you need to take to make the weapons. Then the fact that the material and step in making each weapon is different according to the material and weapon type.
Les Yay: Pearl blushes and gets self conscious in front of the female hero, and Esmerelda develops a tiny Bodyguard Crush towards her as well. Granted, since gender has minimal effect on in-game dialogue, this also happens with the male hero. Sandra exchanges suggestive dialogue with various female Jumi, and then there's her relationship with Florina. Daena is said to love Matilda like a sister, but there's a little room for speculation.
That One Boss: Boreal Hound. His level scales with the players and he has multiple attacks that can only be dodged if you're lucky. Plus he goes invulnerable when he's charging his attacks - and he charges so frequently it's tough to finish a combo to stun him and pull off your own big move. He's moderately difficult even on the normal Easier Than Easy mode, and if you meet him in No Future Mode? You'll need that gamebreaker sword...
Tropicallo. He's a plant monster with two heads - a "fighting" head and a "magic" head. You knock the heads off the main body, kill them, and each dead head drains a bit of Tropicallo's life. The thing that makes him hard? The magic head, after getting knocked off, releases an area-of-effect magic blast that one-shot-kill you. It may not be too, too hard to avoid, but when you literally have no room for error, "not too hard" can easily become "way too hard".
Player Punch: One per major story arc, as horrible things keep happening to the characters you grow to care for either as a direct result of your actions or because you weren't strong enough to protect them.
Replacement Scrappy: Aura for Luna. Because Luna (the moon) and Dryad (trees) were the elements with no opposite, LoM ditched Luna and created Aura (metal) to be Dryad's opposite. There's nothing wrong with Aura per se, but just getting rid of Luna like that annoyed part of the Mana fanbase.
Tear Jerker: Most of the arcs have at least one or more major ones. The Junkyard and the Jumi Storyline especially are often cited as a source of actual tears.
Tier-Induced Scrappy: Among the weapons, the spear kinda... sucks. It's supposed to be a long reach weapon with a 4 hit combo, but the 4th hit in the combo has less range than anything besides a punch, which means you have to get in close to combo-stun. But it's still slow to swing like the other long reach weapons.
The Woobie: Too many to name. Larc, Matilda, Irwin, every single Jumi, Elle, Bud and Lisa, Rachel...