I try to design my levels as naturally as possible, but of course, realistic level design would mean that it's all just some flat area with possible platforms being branches or something. It all depends on the tileset you are using and the area you are trying to create, then try to think of ways to still make the design interesting. Basically, what Strato said, too.
In the original levels, Colonius would have some parts where the sewers are sort of built into the houses and rise above ground level; that's unnatural.
For natural design, I'd give you a shameless plug for Fragile Existence, but since that has design flaws... study Evil Mike's Invasion of Deserto packs.