The skeleton will cause problems if you try to scale the whole model. The eyes can just be moved around to the correct position, but it’s hard to get it exactly right all the time, due to the aforementioned skeleton issue. The hands are the same thing. Probably leaving his the same size is your best bet to avoid skeletal weirdness, and most SF4 characters have disproportionately large hands by default anyway.
It’s most likely a compression issue. You need to open the original DDS in Nvidia’s WTV tool to see what kind of DXT compression they used and then save yours with the same level of compression. If you have the same resolution and the same compression, they should come out to exactly the same filesize.
Something has gone wrong if you still have a *.cos.emz file afterward. Instead, you should have a RYU_01.bsr, RYU_01.nml.emb, RYU_01.obj.emo and RYU_01.shd.emo. For the model tweaks, the obj.emo is really the important one.
Yes, semi-transparency only works on DXT5. However, the hi-res files I made for Sakura have been modified to accept DXT5 instead of DXT1.
Glad you got it going
lol @ the endian change. At least you figured it out. I get stumped by that kinda stuff and never get past it.