Well, when I started for IL2, most often requested was a 3d model viewer, so that we could quickly check how the skin is looking without launching the entire game. Some people (myself included) were able to task switch between IL2 and our paint program, but many others could not.
I really like the reflection maps that I found when I started working with FS2004, some interesting effects can be done with that.
Also, in many cases the rivet/panel line voids from IL2 were quite good, but had to be remade because they were stuck on the background. If they had been avaliable as a PSD with the rivets and lines on a separate layer, it would have saved some work, especially for new guys. Unfortunately with many, many aircrafts in IL2 releasing this many PSDs would have been likely impossible.
Lastly, I often recall that in game online play with IL2 suffered from having to transfer the uncompressed skin file through the network before it would show up. Now, in the early IL2 days, this was OK, even on dialup as the skins were only 256k each. But with FB, now each skin was 1MB and almost never would some people's skins finally appear in game to other players! There was often talk about having the game "compress" the skin files before sending them to the other players PCs to save transfer time.