The complete changelog can be read in CHANGES.WII in subversion, these are the most important changes.
Emulation speed has improved a bit
Keybindings have been improved and extended (commodore key, del etc) and now behave more like the real keyboard
Added support for the classic controller. Note: this is untested since I don't have a classic controller. Please test and fix bugs in this part!
Add support for loading .prg, .p00 and .s00 files. Only .prg has been tested so the others might not work.
Various glitches and small bugs (long filenames, sound in menus, frequent prefs saves etc) have been fixed