I'm not sure if I'm posting this in the right place, so feel free to remove it if this kind of question is better asked somewhere else.
My ultimate goal with Adobe After Effects is to be able to create animations like this using real people: PGSM All Transformations - YouTube
I'm really not sure where to start, at all. What are the key skills I should be learning / refining to move up to something like this? What would I need to keep in mind while filming?
The first things to do would be to get a solid foundation in how to work with After Effects. I would recommend against just jumping around to random YouTube tutorials. Pick a good, solid, instructor. You could do a class on Lynda.com or Digital Tutors, but, if you want something for free, Andrew Devis' beginning AE series on Creative COW is pretty good. It's old, but the underlying way of working with AE is pretty much the same.