They altered the coloration of the graphics, at least. It can look either better or worse than the original palette depending on the scene, though.
As for the new content, I'd have preferred they include none rather than what they did. That it includes some of the most tedious game design in recent memory should clearly mean it has no business being in Chrono Trigger.

Originally Posted by
leader of mortals
(SPOILER)Does this new ending tie into chrono cross or something, because I never played that...
Yes, it does.