The blog post says that Two Tribes very carefully designed every level - Each one had to have its own unique feature or theme, without making the solution too obvious.

The post also reveals some interesting things from this and the previous Toki Tori - For example, Toki Tori on the GBC could not display more than two enemies on-screen at any time (Meaning no levels had more than two enemies), and, originally, due to an error in programming, certain enemies in Toki Tori for WiiWare moved faster when walking to the left than they did walking to the right.

If you want to find out the whole level design process, read the blog entry!