I have been thinking about this a lot, actually. Nothing will be changed for 3.0.3 as we're close to wrapping that up but I do have a few ideas.
My first one was to set a flag to note that a skin needs recaching instead of actually recaching it. This would mean that when the skin is loaded, it would check to see if it needs recaching first and if so, then recache it. This effectively distributes the caching over several page loads. The downside is that there may be times where an instant recache of one skin is required. I'll have to look into it more before committing code changes. Most likely we'll introduce the flag system along side the instant recache system.
Real Deal reacted to Matt in [Suggestion] Skin Caching on Parent Skin
