Well, when he first released the 5th Gen version, there was an issue that affected Bond697 and I where an extra ribbon from previous gift data would remain, so the output Pokemon was hacked. IIRC this has already been fixed. Then there are those bugs where the program just doesn't work for some people, e.g. program doesn't launch.
I'd actually prefer using PokeGen, if I don't require any functions that are in MGE or if the functions are on par. This is because PokeGen has all the functions in a tab format or easily accessible within 2 clicks at most, this makes it very user friendly, etc. Not to mention it's a shortcut on my Quick Launch, lol.