http://www.mpc-forums.com/viewtopic.php?t=78018
Nothing besides looks, but the LE was produced later (2000), and therefore newer. And I think all LEs are equipped with the VGA expansion board as standard, but I'm not shure about this.
Some, including myself, think that 3000 is better sounding than 2000/XL (I used the Xl for some years and then went to 3000LE)
I dont know what you mean by making beats in Pro Tols, but you can have the 3000 as a sequencer for sounds in PT, or use 3000 as a sound module for PT, both via MIDI. The 3000 is a great sequencer, and has 2 MIDI ins and 4 MIDI outs.
The 3000 is for shure a dope machine for drums and samples, and I use it for bass too. It is a bit more old school then the 2000 as you trim samples by numbers instead of waweform editing.
It has 32MB max sound memory, and is 16 bit stereo 44,1 Khz, just like the 2000. The 3000 has a lot of the same components as the 60/60II, and the same AD/DA converters, but the 60 stores the samples in 12 bit non-linear at 40Khz.