We have seen more than a few ways to integrate 2D and 3D elements together after the fact when using After Effects. Techniques can range from using Cineware, to scripts that will send relevant data over from 3D to After Effects, to 3rd party plugins.
One such plugin, Paint & Stick offers in interesting workflow that give you an interesting look, and also save some time by rendering less in 3D. Paint & Stick lets you paint directly on 3D renders in After Effects, while also providing an animation toolset that is sadly missing from Ae. You can onion skin and use photoshop brushes, like a more natural 2D animation production tool.
An example of this type of workflow is how Content Creatures recently used Paint & Stick 2 on an in-house brand film for the studio. Andy Williams, the lead animator on the project walks through how he used the P&S tools to create an organic hand-drawn texture to the animation, and add 2D people to a 3D scene. Paint and Stick was used to link the 2D and 3D together. Content Creatures noted that doing it this way, (rather modeling characters in Cinema 4D) was a real time saver.