The main idea behind Cocoon is the concept of pipelines. Cocoon 1.x and 2.x applied this idea with a focus on web applications. But sometimes pipelines would be useful although you don't develop a web application. Those former Cocoon versions don't really help you in that case.
In contrast, Cocoon 3 follows a layered approach so that its basic module - the pipeline module - can be used from within any Java environment without requiring you adding a huge stack of dependencies.
On top of this, Cocoon 3 has the goal to make the development of RESTful web services and web applications a simple task.
Cocoon 3 has been built completely from scratch and doesn't have any dependencies on Cocoon 2.x or 1.x.