I like skins because they're cheaper than geneing up my dragons. xD; For instance, this guy:

Try loading him up in the Scrying Workshop, his ID is 89828. Quite the looker, right? His primary and secondary are pretty unfortunate, and his tert just won't go well as anything. I'd have to spend a ton of money on Scatterscrolling him into new colors, and theeeeen shell out a ton of money for genes to make him pretty enough to match his mate:

Oooor I could just stick a skin on him. BAM, instantly pretty Imp.
But I do get what you mean about it being a shame to cover up already pretty dragons. o: Like, the dragon is already pretty, why cover it up? I usually just put full skins on the dragons I haven't yet made pretty. xD;