I know I am coming in a bit late on this thread, but after looking at that image of the photoshop layers, I suggest training your friend
on how to prepare a Photoshop comp for After Effects. When working with other designers, especially print designers, i always make sure we are on the same page regarding prepping Photoshop files for AE. There are so many ways to make a file more efficient in AE.
for instance... separate layers for each shadow? Why not just throw a single light on the whole scene? or generate the shadow with the
Drop Shadow effect. Definitely combine as many layers as possible. It is just part of the job for me. I try to manage expectations with clients by requesting that files be prepped for AE if possible, just so they know there is effort required there. That usually leads the conversation to the difference between Print and Video and just generally helps in client understanding. Remember that you are the one that needs to have files made a particular way for your personal process. It is ultimately up to you to educate the designers and clients you work with, or be prepared to fix the massive photoshop files that come your way. They can't be expected to know what you need until you tell them. I am not sure how much of what I just wrote is applicable to your problem, but i am pretty sure it is not entirely a software problem. I have found it sound advice and useful in many cases. Animation is hard to do well, and nothing worth doing is easy. Just get excited about it. It beats flipping burgers! (unless you are hungry)