I'm not 100% certain, but I think the MKII also has more EQ control. I had an original 488, but it only had a treble and bass tone nob for each track.
The 488 is a great machine though. The only downside for me was that you can't record more than 4 tracks at a time on it, and I was mostly recording my band. For a singe person - aka a one man band setup - it's a great machine.
-MD