Thanks to Capcom's decision to forego emz containers and their associated headaches, moveset swaps are extremely easy to do now and they're not plagued by the "monkeyface" problem we all know so well.
Here's how you do it:
Step 1: Make a backup of your AE installation. If you mess something up, this will save you a lot of time, I promise.
Step 2: Pick 2 characters: 1 whose moveset we'll be taking (the donor) and 1 who will be receiving those moves (the recipient). For this example, I will use Hakan as the donor and Ryu as the recipient (i.e., Ryu with Hakan's moveset).
Step 3: Go to the resource/battle/chara directory and find your donor's folder, in this case HKN. In this folder, copy all of the files from HKN.cam.ema down to HKN.vfx.ttex.emz EXCEPT for HKN.fce.ema and copy them somewhere (a working folder where we have write permissions is appropriate).
Step 4: Rename all of those files we just copied to match our recipient's character prefix, in this case RYU. Now, go back to resource/battle/chara and copy them into our recipient's folder, overwriting the ones that are already there (it's cool, you backed everything up anyway, right? Right??).
Step 5: Now, this is the key step: navigate to your donor's "latest" moveset files, which are located in dlc/03_character_free/battle/regulation/latest/ for normal characters (I'll update this post with the AE character's locations when I get home). Take the donor's bac and bcm files, in this case HKN.bac and HKN.bcm, copy them to our working directory and rename them to our recipient's character prefix.
Step 6: Finally, we take our renamed bac and bcm files and drop them into our recipient's folder in dlc/03_character_free/battle/regulation/latest/ (assuming they're a normal character and not AE-specific), overwriting what's there.
That's it. All done!
I'm going to explain a little bit about what we've just done, so read over it if you're interested:
The actual moves and animations are stored in the .bac and .bcm files, which were previously components of the *.cmn.emz bundles in vanilla SF4. When they were bundled, we had to open the entire bundle in a hex editor and find the desired files and names to edit manually. However, since Capcom stopped using the bundles, we can just rename the files and be done with it.
Now, you'll notice in step 3 we omitted the *.fce.ema file, which contains the character's face animation data. By doing so, we've let Ryu--our recipient--keep his original face animation data, thus avoiding the monkeyface for the most part.
Last, I wanted to mention the various revisions of moveset files included in the AE installation. The ones included in the resource/battle/chara directory are the regular, non-AE movesets, which are superseded by the ones located in dlc/03_character_free/battle/regulation/latest/. However, during the challenges/trials, the game reverts to using the SSF4 movesets, which access the resource/battle/chara ones.