Tried looking for an Ys thread way back, but didn't try hard enough. Much easier to find now since I looked when it was bumped.
I've only beaten Ys 1 and 2 Chronicles, Memories of Celceta, Ark of Napishtim. I've only played Ys V, but I've never finished it. I only got a PC a couple months ago, so I've yet to buy Oath and Origin yet (and I'm most excited for those).
At this point, ranking them would make me feel bad. Ys 1 definitely is the weakest for me, but when you combine it with 2 and see how it concludes, it feels pretty special. I'll admit I wasn't too interested in the party system in IV or the dialogue at the start. I even turned the AI to evasive so it felt like a solo game for a bit, but switched it back and warmed up to it. I actually enjoyed switching characters midway through too.
I'm mixed on how much story there was. I mostly minded it at the very beginning, but I started enjoying it once you reached the other side of the river (I didn't enjoy where I'd have to talk to most everyone in the village portions). Also, it took me awhile on realizing that the two Frieda was talking about were the characters that would appear in VI. Favorite part was probably the adventuring for me while my least favorite was the ending. I got way more out of 2 and 6's endings.
As for 6, I know people generally see this as the weakest of the Ys games after the hiatus. I can see why, but I still got a lot of fun out of it. It helps that I waited for the Steam version. Out of the games I've played, certainly my favorite regarding NPCs over the course of the story. Unlike Celceta, there were only two towns, and they were both affected by the ongoing story. Also I liked how it tried to connect the lore with the previous games towards the end again.
Last boss I didn't mind. I liked the quirky boss music and I considered the boss before that as the real final boss while this one was a fun extra to me.
Oath and Origin were the two games I wanted most when I was waiting to get a PC, but I'm still going to hold out on a sale. I might play Seven next, but I've shifted gears to Nayuta no Kiseki. The beginning is brutally slow and talkative. In Celceta, minus the tutorials they made me do, I was fine with the beginning. I hope Ys never goes to Nayuta's lengths ever.