Just how much corruption is known. Even if you make the assumption that people in aggregate can generally assess whether corruption exists somewhere, it'd be harder to measure the 'severity' that way. I actually think you're probably correct that people's perceptions of corruption have some connection to reality, but I think the more fundamental problem with such a scale is boiling a complicated reality like corruption into a single corruption number, which seems pretty silly on its face.
Up to a point. A lot of these indexes are PR and the people who answer them have motives to rate one way or the other (e.g. you are an opinionated journalist and you want the current government to look bad).
There's usually something weird going on with some of these indexes if you compare statistics with opinion-survey-based stats.
Look at crime statistics versus how safe people feel. People say “crime is worse than 20 years ago” when the murder rate is 1/5th.
Perception =\= reality.