Does anybody know the name of the superbattle droid's skin? Apparently I chose the wrong one.

cis_inf_sbdroid.tga should be what you're looking for.
That should be located in BF2_ModTools\assets\sides\cis\msh

if you have the SWBFII msh Viewer you can open the tga file and klick on the "I" button than a new window pops up showing you what files are used for the msh

Is cis_inf_sbdroid.tga supposed to be mostly transparent? It hardly looks like anything. In fact, if I start messing around with the entire image's hue, only the little red light changes color.

Is there something special about skinning super battledroids?

If you are using GIMP, then check out the following:

[b][color=#FF8000]The FAQ / Everything You Need Thread Version 2.0[/color][/b] wrote:...
Skinning
...

• How to work with alpha channels in GIMP(video tutorial)
• Dealing with alpha channels in GIMP(written tutorial with images)

...

Thanks, I guess that's what I'm looking for.

so if you have not gimp, you could use PS or PSE that manages it automaticaly, but has sometimes problems with the save funktion. combinated with Paint.net and the PSE addon for it i'm going good.

SO if you cannot remove the alpha channel i could do it for you But you should try it for your self first