Looking at gameplay videos of the arcade game, there is at least one addition not present in the 3DS iteration: multiple touch notes that you need to hit at the same time. The 3DS format should be able to represent that, but I wouldn't be surprised if they were subtly different.
There was also a (now defunct) iOS game, which notably had a "Compose Scores" mode to edit your own tracks (though you couldn't change the BGM). I would be curious to see what the editor interface looked like.