Animation codec is lossless and was never intended for playback. It's a production codec designed to move files through the pipeline without introducing compression artifacts every time the file is modified. If the VLC player is playing it back smoothly then that's a lucky break because the data rate of an HD Animation Codec movie is higher than the maximum read speed for most hard drives.
As Rick said, animation isn't necessarily meant to play in realtime. The rest is not relevant. There is nothing missing, something is wrong with your QT install like e.g. hardware acceleration not being enabled/ not working... Reinstall, check the relevant system control panel.
Sorry, I just realized I wasn't entirely clear as to what my problem is.
I was thinking the quicktime issue might be some insight into why it the Animation codec crashes After Effects.
The problem is that I do use Animation codecs in my production pipeline everyday. I had no probem bringing these files into After Effects on my old machine at work.
I'm now working on a new machine at home and whenever I try to edit/export a Animation codec MOV. file in After Effects, it completely crashes my system.
The farthest that I get is that after effects will import it into its library, but as soon as I try to put it into a comp, system crashes.
I also really don't want to convert the codec in another software purely for saving me lots of time.
What is your OS and your version of AE? Do you have any 3rd party codecs or codec packs installed? What is the version of QuickTime?
I have no problems on any of my machines and I have only heard of random problems involving 3rd party codecs and a few problems with QuickTime pro installations.
Windows 8 pro
AE CS6 & CC
DivX Codec Pack (however, wouldn't work before I installed this either)
I have also uninstalled and reinstalled Quicktime with no luck.
As an update,
I have since uninstalled AE CS6, CC, the DivX Codec Pack and Quicktime.
I reinstalled quicktime first, then AE CS6 and CC
and I still have the same crash problem.