Ys II ends with what was supposed to be the elimination of all magic with the Black Pearl. However, you still see the occasional mage or the like in later games — they're rare, and magic stored in or channeled through items is much more common, but you still see them. How does this work?
There are other artifacts that enable magic in the world of Ys, i.e. the bracelet of Genos. The sealing of the Black Pearl only eliminates the magic that comes from the kingdom of Ys such as Adol's magic from Ys II.
Speaking of, why is there a mage class in Ys Online? Magic users have been rare in the series to start with, and then there's the loss of the Black Pearl. It's a few centuries later, but the series has generally gone in the direction of less magic as time goes on, not more.
The Black Pearl isn't the only source of magic. Also, the settings in the Ys series are prone to change so it's not particularly egregious.
Oh, dear lord, Mask of the Sun. It takes place two years after the original Ys — the same time as Ys III, give or take. That could be handled, but it also shows Adol as still in Esteria when Ys III and the ending of Ys II established that he had been traveling. Then there's the fact that Ys III established that he'd been traveling with Dogi since the end of Ys II, but he leaves without Dogi in Ys IV.
Although it's canon for now, Mask of the Sun isn't developed by Falcom so there are some plot holes. Expect Ys IV to be given a complete overhaul when Falcom decides to develop it themselves.
Not to mention the fact that Ys IV is canonically set between II and III.
Adol has destroyed two entire mythical civilizations, laid low the schemes of the Romun Empire at least twice, and killed enough dark gods to fill a pantheon. At some point, you'd think those villains who aren't said dark gods who have been sealed away for millenia would pause for a moment, and go "You know, whenever anyone tries something like this, it ends with Adol destroying their plans utterly. Maybe it's best not to even bother."
Oh, the good old Villain Ball, without it though, there would be no story.
Why does Adol never bang any of the girls he meets? He should know that he isn't immortal, so leaving behind his seed would be wise of him. In the case of Feena, Reah, and Lilia, all three of them were clearly interested and I doubt they would have any objections.
He is a traveler... I don't think he really had a chance to settle down as far as we've seen. Otherwise... it would be a little bit too cliche as any standard RPG.
In Toal Fact's story in Origin, it's flat out stated that destroying the Black Pearl will kill the person doing it. That's why Feena and Reah insist on sacrificing their wings to seal it rather than letting Toal destroy the Pearl and take the Demonic Essence with it once and for all (Reah being willing to sacrifice herself for Toal and being unwilling to let him sacrifice himself for her). And yet, when the goddesses wake up 500 years later, they tell Adol to destroy the Pearl without hesitation and all that happens to Adol is he loses the ability to use any magic that was derived from the Pearl. What happened?
Most obvious explanation: That was true then, when the Pearl was at the height of its power, with an entire civilization using its magic and feeding back into it. When Adol comes across it, it's just re-emerged after being sealed for five hundred years, there are only a handful of people with the magic of Ys, and it's greatly weakened.
In Felghana, how does one logically explain the fact that the only part of the mine where monsters drop Raval is the part of the mine that is played out? Shouldn't the ore be more accessible in the section where there are still workable veins?
Maybe it's played out because the monsters ate what the miners didn't find?
The prison in Darm's Tower known as Rado's Annex was called that even when it was first built, but there is nobody named Rado in Origin. Where did the name come from?
Why are the Books of Ys so inaccurate? There is no mention of the Black Pearl in them whatsoever. Furthermore, Priest Fact talks about nobody knowing why the demons and goddesses vanished at the same time, when he knew exactly why this occurred, as he was there when it happened. He also makes no mention of his predecessor's involvement in the demon's attack.