Oops, misread your post and wrote a reply thinking you were talking about Ys I&II:
The only nice thing about the PS2 versions is that your level carries over from Ys I to Ys II. Otherwise, the extra content is totally not worth the low-res trade-off. Just use a PS2 controller and play the superior PC versions and you're set. (For Ys I&II, I might even just suggest the PSP version -- it's kind of the best version overall, since it has three different sets of music.)
Regarding Ys 6, the PC version is superior to the PS2 version, but the PS2 version gets the job done at least. Steer clear of the PSP one though - it's crap. Also US voices in the PS2 one are awful, so if you play, definitely play with JP voices. (Or just play the PC version, since it's better anyway.)
Felghana is my favorite of them all, I think. So, so good. I'd probably rank the series something like this (note that I haven't played Origin yet so that's not in here):
Ys: Oath in Felghana (PC or PSP)
Ys IV: Mask of the Sun (PC Engine)
Ys I&II Eternal/Chronicles (PC or PSP)
Ys 6 (good on PC, kinda so-so on PS2, awful on PSP)
Ys IV (SFC)
Ys V (SFC)
Ys III (old version)
I'm probably forgetting stuff here and there, but generally speaking, that's how I remember it. Also, Ys I&II is up there mostly for nostalgia. Overall it's not half the game Ys 6 is, but the memories are just so good.
(If you play it just for the music, the best music of all the versions is in the PCE/TG-16 version, BTW.)