Setting-wise, though... call me morbid but Shadowrun is kind of too "Happy Bright Future" for my cyberpunk tastes. Nowhere near enough despair and dystopia. A cyberpunk-supernatural mashup I could totally dig is Cyberpunk/Cthulu.
Same here, I'd prefer less high fantasy, more occult. And Shadowrun definitely pays more lip service to cyberpunk themes than they actually support it in game terms.
If we're talking about a Shadowrun game with a different Shadowrun setting, where Cyberpunk and Magic are mashed up, I think I would just like a setting that's more tightly designed, to be honest. Instead of a setting where Tech and Magic are blended all over the place (despite what the books say about them not playing well together), I'd like a tech-heavy setting where magic is rare, lower powered, and represents chaos in a world obsessed with control. So it has a cyberpunk purpose, because it's f'ing magic. When magic is powerful and you need magic to fight magic and it boils down to just another dimension of combat, it becomes ubiquitous and predictable and it ceases to be magic for me.