All Ys games are self-contained despite having an order. Ys 1 & 2 are really the only ones you should play in order (and luckily, they come together). As far as best story, I think Ys 7 has the best story, Origins or Memories of Celceta has the best gameplay.
If we're talking PC only, then Origins or Oath in Felghana.
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Gameplaywise, I feel like Origin's the best. It runs on the same engine that Oath in Felghana does, though it's a little more polished and has a bit more variety in your options on account of having three playable characters. The difficulty curve is a bit better, too-at least for Yunica, who plays the closest to the series' standard protagonist. The other two characters have a few things that make the game trivial. Oath in Felghana, meanwhile, has more enemy and environment variety. It's also harder overall.
Ys 1 and 2 use the "bump system" which involves sacrificing the attack button in favor of running into guys over and over. This might sound bad, because it is. The second game gives you magic, which helps with it a bit, but it was silly then and it's silly now, nearly thirty years and almost as many rereleases later. The games are short enough that this is tolerable, at least.
Story, again, Origin's probably the best. It ties a lot into 1 and 2, with some shared plot elements/enemies/music/etc., but it's not necessary to play 1+2 to follow what's going on in Origin or vice versa. (Playing one helps the enjoyment of the other, though, I'd say.) After those, though, the rest of the series is just Adol going on various unrelated adventures.