Also in Time's Arrow they could tell it wasn't Lore because Data had an 'L type brain'.
I think the problem with Lore is that Soong tried to program more realistic emotional behavior.
Given we've seen how holograms can be created with perfect human emotions and ambitions (moriarty), it strikes me that its probably not difficult to "scan a human brain and make a duplicate of emotions." It's just that Soong's positronic brain/android body makes a figure more inclined to be like Khan or the Augments.
Supermans rarely have humility or compassion. Data without emotions gave him time to adjust to ethics.