The DLC sections would have been more heavily criticized (especially Chapter 6), which would have hurt it.

The real key factor, however, is that it came from Square. It wasn't specifically that it came at a time when there was a dearth of good JRPGs (because there are some fantastic ones, especially for the DS and 3DS), but rather it came at a time when Square had stopped producing fantastic JRPGs. While Square is no longer the company it was, the titles still hold considerable market sway, through name recognition with those unfamiliar to the genre, and through nostalgia with those of us who grew up with the Square RPGs at the time they absolutely ruled the JRPG market.

Had this game come out in the SNES era... It would have utterly shattered us all and been the best selling game of all time for looking so gosh darn fantastic at a time when we're all still using sprites and low resolutions.

However, ignoring the visuals and concentrating on the game, it wouldn't have changed so much, because it would have been "just another great Square game". During the era of Chrono Trigger, Final Fantasy VI, Final Fantasy VII, and Super Mario RPG, it would have fallen among the crowd. A fantastic game and well received that only got more popular over time.

The big danger is that Square would have overlooked it. It would have the same reaction to them: "Wow, our games are printing money, what should we make next?". We either wouldn't get a sequel, or we would get another Chrono Cross, a game that tries so hard to create its own experience that it ceases to be a good sequel and isn't as loved as it should be because of that.