At least when Trillian ditched skins, I think they were trying to compete with the bigger players (MSN, Google Chat) more seriously in the business world, and skinning isn't really something businesses care much about. In fact, just having this feature available can make the app seem more juvenile and less appealing than more "serious" alternatives.

Plus, you have to keep adding skin support for every new feature you add, which means the many skins that don't keep up will no longer work for the latest version of your app, which pisses off users. And when skins slow down or stop being made (people get bored, move on) it reflects poorly on the app, making it look like a ghost town.