You need to think about the Earth as a dynamic planet that is always changing. New spreading oceanic crust near the spreading centers tend to be higher in elevation than the older crust nearby as the material contacts as it cools becoming colder and more dense. Then as this older material collides with another oceanic crust, one will subduct below the others, which can be observed as a trench. Other processes such as under-water currents or turbidites can lead to uneven distribution of materials. Storms on the surface, mass wasting, deltaic deposition by rivers, activity by critters and changing in global sea levels and erosion all make for an complicated environment.