Unique to this version are changing background audio and visuals as you level-up your game, providing something new to distract you while playing. Whether this is a good thing depends entirely on your personal preference and ability to multitask. If you're one of those that simply needs lots concurrent stimuli, you're likely to prefer this version.
On the one hand I do like some of the audio choices. I enjoyed it so much that I even kept the game open and playing while writing up this review. That being said, the song that comes in with the second level is quite irritating to me, and yet it just made me want to play faster to get beyond it. The changing audio and visuals makes the experience somewhat reminiscent to playing the original Lumines game for Sony's PSP, though not as well done.
Still unchanged, however, is the use of the insidious Flash custom cursor which, although aesthetically pleasing, does more to degrade the experience than add to it (Update: I just received word from Game-Pure that after reading our review, a new version of the game was made to allow you to select a normal cursor on the title screen! Arigatoo gozaimasu, Game-Pure!). Also unchanged, as Uri Arad pointed out in the comments, is the fatiguing click-drag interface. Still, I can't stop playing this game in all its iterations, which indicates the annoyance as minor when all things considered.
Cheers to James for the alert about the new version. =)