The hardest part for me are the colors (like text, button face, etc.). It is hard to tell what color does exactly what. Everytime it is trial on error. Would be nice to have clear docs about that.
Also very hard to do is to make the skin compatible with older versions of WB or different flavours of Windows.
I use both SKS and a text editor. The naming conventions of the raw format are erm... a little odd to say the least.

SKS does a good job in hiding that.
Most sections work the same (i.e. have the same basic ingredients), but a lot of sections do not work like you expect. SKS is a great help for those.
WB is notorious for not fixing bugs. Some of these bugs are there for years. Recently I have given up reporting bugs and I'll try to find ways to circumvent them instead.
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