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.
Cliché Storm: The plots of the various games often face accusations of this. When the series was new, they didn't have as much teeth (since the entire medium was still newish back then) but most people agree that it got a bit more true with Ys V and VI, and the older games do suffer a bit now. As for Ys SEVEN, much like the gameplay is significantly changed up from previous installments, the story deliberately sets up an apparently cliche experience and then proceeds to turn player expectations completely on their ear on just about every front.
Complete Monster: Cain Fact in Origin. Cain is the one responsible for allowing demons to invade Ys, causing it to float. He also uses his own sons in an experiment to see what would happen if a human is imbued with seeds of evil. Later, he fuses himself with the black pearl and becomes Darm, the main antagonist in Ys I and Ys II.
Also, Bishop Nikolas Garland in Oath. He played both Count McGuire and Chester like fiddles to bring about the resurrection of Galbalan, AND he shows nothing but contempt for Nell after Nell happily serves him as "Dularn" all throughout the plot and gives her life to try and stop Adol.
Demonic Spiders: The enemies in the lower mines in I, especially Eternal, mainly due to their high speed and power coupled with the limited visibility, and the Elite Mooks in the upper levels of Darm Tower, which quickly mow you down even if you have the Infinity Plus 1 equipment.
Don't forget the literal spiders in Ys 6 right after the first boss. They do intense damage, swarm at you and stun you into infinity, and the only way to kill them easily is to do a drop attack, leaving you open to getting stunlocked from ones that the drop missed.
Bigger versions of those spiders appear later on. They are just as bad.
Ys III being by far the most widely released Ys game in the U.S. at this point (first on all three fourth-generation consles, and now on the PSP) also doubtlessly helps her overseas.
Goddamned Bats: The near-literal bats (Invincible Minor Minions until you find the Bell) in Limewater Cave, the Adol clones, which are really tough unless you use the Rainbow Fragment to reveal their true form; the boss Orjugan also summons them on higher difficulties; the scorpions in the underground areas (some of which are invincible on Nightmare), and the dragonflies in the Ruins which shoot in a circular pattern, easily knocking you off the narrow platforms. And the color-coded enemies on higher difficulties, which require you to use the right color Emelas sword on them.
Moral Event Horizon: During Hugo's scenario in Origin, Dalles not only petrifies Epona but also shatters her to pieces right in front of Hugo.
In Yunica's scenrio, Zava crosses this when she kills Roy right in front of Yunica.
Seinfeld Is Unfunny: 1UP called the original duology one of the most boring games of all time in 2004. It isn't hard to see why - it's an "action RPG" where you don't actually actively attack much of the time. Even by 1988 it was getting stale, and the next three games were all about essentially trying to find Ys' footing in a new world with lots of competition. These days, seeing what made the games significant in any way can be extremely difficult (I.E., the impressive-for-the-era graphics, amazing music and the fact that the games were voiced at all - nowadays, meh; in 1990, absolutely mindblowing).
Sequel Displacement: If you ask a Western gamer to describe a Ys game they know, assuming they know of the series at all they're most likely to describe a girl named Elena, a Jerkass named Chester, and a town called Redmont - Ys III is the best-known of the Ys games in the public eye, due to the fairly significant amount of promotion the game got and the width of the release, on all three then-modern consoles, followed by the recent, well-received PSP remake. More recently, a fair number of people may describe Ys SEVEN. Just about nobody knows of or remembers the original games, though, despite their TG-16 release in the U.S. (Nobody remembers Ark of Naphistim, for that matter.)
Shocking Swerve: Ys SEVEN pulls this off in spades once you reveal the real main villain of the piece... that is to say, Tia. All of a sudden, a lot of people you thought were enemies are now victims, several people you counted as friends are now out to kill you, and even the characters can't believe whatjust happened.
Tastes Like Diabetes: The Loo (or Roo), if you ignore the cuddly character sprites, the Loo are the only innocent and cute creatures of the series.
Tear Jerker: Most scenes involving Stoker in Ys V, especially with that sad "Theme of Lovers" music. Tia's theme in SEVEN.
Eldeel's leitmotif in Dawn of Ys, which emphasizes his Fallen Hero status and Leeza's feelings toward him.
The ending of I and II, where Feena and Reah leave for a higher plane of existence. "Always remember the girl in me". The sad music "A Still Time" intensified it.
The ending of Ys SEVEN. While Tia is fading away after her defeat, Maya shows up and speaks for the first time, telling Tia not to disappear.
Hugo: Why?! Why did you go through all this... for me?
Epona: ... I, don't actually know...
Even more painful was Feena and Reah sealing the Black Pearl in Toal's route. He's lying wounded and exhausted on the floor, begging them not to do it as they sacrifice their wings to stop Darm. This is made even more painful by the fact that it was implied that he'd found another way to stop the demons earlier but hadn't had the opportunity to explain his plan before the end.
That One Boss: Most bosses in Ys I Eternal, especially Vagullion, Khonsclard (Luck-Based Mission :cough:), and Dark Fact. Most bosses in Nightmare difficulty in 3D Ys games qualify as well.
Gruder's One-Winged Angel transformation in Mask of the Sun. The hardest boss in the game, and it doesn't help that you have to go through a long unskippable dialog before the battle.
And that centaur guy you fight on the Minea Plains, who Turns Red halfway through the battle.
Karion, and Jabir's One-Winged Angel form in Ys V, particularly the Expert version. Both are battles of attrition, need plenty of healing items.
Nightmare Orjugan in The Ark of Napishtim. This boss was the hardest in the game, harder than Nightmare Ernst, IMO. And Nightmare Napishtim's first form, where the Frickin' Laser Beams are faster and take off half your HP (the second form is pretty much the same as lower difficulties, just with more HP and reinforcements).
Vagullion in all versions of Book I (swarm of Goddamned Bats that coalesce into a gargoyle, you only have a split second to hit him without taking damage)
The crystal boss in the Cursed Mine in III. Even with the Time Ring, this fight is a royal pain in the ass.
Darm in Book II. Basically Bullet Hell in an RPG, and a battle of attrition. Ironically, they made him easier in Eternal, where every other boss is That One Boss.
On Nightmare difficulty in Ys II Eternal, most of the boss fights are Bullet Hell. Nightmare Zava(Yetai in the Turbo CD version) takes the cake as one of the hardest bosses in the series. She was hard enough in the original.
Arem's first two forms in Dawn; he's fast and hard to hit, his shots are really hard to dodge, your attacks do hardly any damage even at maximum EXP, and it doesn't help that he can regenerate his HP. And the Ice Boss in the same game, who can only damaged when he splits into a fast-spinning circle of crystals, and only one of the crystals can be damaged.
Khonsclard (again) in Origin; Multiple targets (both his main body and several star-like enemies, the latter of which heal him if you expose his weak spot by way of attacking his main body instead of taking out the stars one by one), lots of projectiles (all of which are VERY HARD to dodge), the stars multiply as the battle progresses, AND he constantly pulls you toward him. Dalles is NOTHING compared to him.
They Just Didn't Care: Basically every third-party port or remake has at least a few moments of this, though it's nicely averted in the Korean-made Ys II Special where the designers obviously did care.
Woolseyism: XSEED Games seems to specialize in this with its English localizations, such as with the random Castlevania: Symphony of the Night reference in SEVEN from a minor NPC, and more recently Ys I & II Chronicles renaming Dr. Buldo and Slaghf to the easier-to-pronounce Dr. Bludo and Slaff.
XSEED had a massive heyday with Chronicles by throwing in every obscure reference they could think of when you hit a civilian with a fireball rather than just a generic angry phrase.