I think it wouldn't be a punish but an add. Especially falling in stairs sometimes would be that much preached realism, and also quite funny.
I'm not suggesting a radical change but a slight disadvantage to otherways so superior solution, if you have efficiency thinking.
You're not punishing building in 3D, you're only proposing that stairs and ramps (vertical movement) be considered inferior to horizontal movement. I'm confused as to how that isn't punishing people for building in 3D, especially given the subject, "Disadvantages to stairs and ramps". It's more realistic, I agree, and might even be funny at times, but I'd rather not players be punished (however gently) for their design decisions.