Those comments are mainly from purists. I prefer the PS1 versions, but I can see the merits of both sides. What it boils down to is there were some story changes, some people really don't like them. The first Lunar iirc had way more changes to it than the 2nd, for whatever reason. There are some other minor things too, like the world map being shrunk down for the PS1 versions. For some reason I think that really bothered some people. Personally I liked that there were no random battles on the world map in the PS1 version. Been awhile since I've played any of them though, so my memory may be a little hazy.
Btw Arc II is awesome. Arc I is pretty good, but required playing for the 2nd. The third one, meh, I wouldn't bother.