If you want users to edit the songs...
You need to increase the granularity of your piano roll tool. There are a vast number of songs where chord changes fall somewhere other than just the beginning of a quarter note. With the limitation of this tool, it is impossible to improve the timing, and many of the songs that come out of your algorithm have mistimed chord changes.
Keith L Morris commented
IF they added the ability to do 8th or 16th notes... but only when you MANUALLY edit a song... that would deal with the problem.
Of course it would be nice to have it to everything automatically... but that is not totally realistic for all things.
But the ability to do a manual edit of the file after auto-generation and display it on the website and in the ios/andriod apps would still be cool.