Well the digital version will definitely have faster load times (already confirmed with Prime 3)I have MP1 and MP2 for GC and MP3 on disc for Wii. What are differences between the original verisons and the digital version of the Trilogy other than adding pointer controls to MP1 and MP2? Are there any other changes?
There were some added VFX in areas like lighting, though some VFX in Prime 1 were removed due to the aspect resolution change and they couldn't be refactored into it (not because of inferior tech).
Here are some more comprehensive lists:
http://metroid.wikia.com/wiki/List_of_Metroid_Prime_version_differences
http://metroid.wikia.com/wiki/List_of_Metroid_Prime_3:_Corruption_version_differences