Before I start, I am the proud owner of a mkII, and did alot of research before buying.
In a nutshell, they used the same external casing, and same buton layou, and just reassigned what some of the buttons do. There are however some major changes along with that.
The main differences are the hard drive space (40 gig vs. 80 gig, the latter being the mkII), the internal drum machine (scrapped entirely on the mkII), the mkII was given a slightly different screen that supposedly is easier to see and work with (though I've never actually used the original so I can't compare)... I know the mkII has a contrast knob to change the display which the original might not have had. There are a few additional effects for guitars also.
The 64-voice GM synth, which was originally accessed and edited via its own fader and associated buttons, located between the Track and Master faders, has been changed. The section has now been given over to the task of sub-mixing, for when up to eight audio inputs are being mixed with the record tracks during mixdown or playback.
On the mkII, the Tap Tempo button, which allowed fast alteration of the speed of delay times and modulation effects, is now the Locate Set button.
As far as I know, those are pretty much the main differences... oh yeah, and the color is different (the most important thing IMO...)