I still haven't been able to fix this
I've been looking at an alternative solution, such as disabling the transformation during the Final Smash.
I've found 2 hacks on this site that do just that, but my game freezes at the stage select screen when I try to load the match. According to the files I've downloaded, they are just simple replacements for the .pac files for Samus and ZSS. Is there any reason why the game is freezing? Do I need an additional code (I only have the File Patch Code right now)?
Here are the links to the two hacks.
http://forums.kc-mm.com/Gallery/BrawlView.php?Number=30464http://forums.kc-mm.com/Gallery/BrawlView.php?Number=30472These "No Transformation" files are PSAs, and the uploader said "These can be used like any other animation", meaning they're regular animations, so if you're a Project M user, this won't work.
Also, I re-read your OP, so ignore my comment on "saving it as .pcs"; instead, look to see if your have both the FitSamus/FitSZeroSuit.pac AND the FitSamusMotionEtc/FitSZeroSuitMotionEtc.pac; if this still doesn't solve the problem, I'd suggest moving this to A/A Help, as that's what this really is.