Cosmetic Mods (skins, stages, etc.)

Create a new directory in your [install dir]\patch_ae2_tu1\battle directory and name it 'chara'. Inside that directory, you can create new directories for any character you wish to mod by using their 3-letter name abbreviation. For example, to mod Hugo, create a directory named HUG. For Ibuki, use IBK. Now, anything you drop into those directories will supersede the original files. If you want to remove a mod, just delete it from that directory and it will default back to the older files.

You can do the same thing for stages, just create a new directory name 'stage' in the [install dir]\patch_ae2_tu1\battle directory. It should work the same way.

Moveset Mods

(Instructions courtesy of DeathrayX)

Capcom decided to "enhance" their game with a fileversionchecker for some characterfiles, like our beloved mvoesets.
This means we cannot just edit akumas moveset and be happy playing with it. Once the game recognizes a different checksum / file it wont load the char and
you are stuck on the battle loadingscreen. :( !

This is the reason why we need USF4 remix from http://www.sf4remix.com/
The latest version at this point is http://www.sf4remix.com/download/complete/USF4REMIX-23092014.zip from 23.09.2014.
This pack contains a loader which helps us with loading our modded movesets.
Step by step:
(1) download this zip file and extract ist contents to the root directory of your USF4 game. WARNING U MUST HAVE REAL USF4!!!
(2) This pack is a mod itself and alters many ingame characters. If you dont want, and want to play with vanilla USF4 chars do the following:
  (a) goto the sf4_remix folder. Then goto battle folder. Then goto regulation.
  (b) delete ae2 folder.
  (c) go into ae2_109 folder. Delete EVERYTHING here.
  (d) go into Super Street Fighter IV - Arcade Edition\patch_ae2_tu1\battle\regulation and copy ALL directorys from here to 
        Super Street Fighter IV - Arcade Edition\sf4_remix\battle\regulation\ae2_109
We now have supplied the USF4 remix folder with vanilla original USF4 chars from capcom!
(3) copy your modded moveset files to Super Street Fighter IV - Arcade Edition\sf4_remix\battle\regulation\ae2_109\***\ and overwrite the existing ones.

You are done so far now.
To launch the game with mods run the remixlauncher.exe as admin.
If you dont like the new hud: goto Super Street Fighter IV - Arcade Edition\sf4_remix\battle\ and delete hud folder.