Something like this is not feasible due to the amount of variables that can occur in a skin.
For something that just modifies resources its possible, but when you touch things such as UIFIle code it is simply not possible.
For example : Ev0 3 uses custom classes and moves the layout of a lot of elements as well a restructuring other parts of WLM.
There is no way you could make a program that would be able to identify where to move things as the change would be too drastic.
Seriously people should stop trying to get spoon fed everything and just try to learn the stuff. It is not that hard once you get used to the terms and how things work
Also its not the Plus! engine thats shitty. Its the restrictions that Windows Live Messenger has which is what makes things bad
(because technically it was never built for skinning).
@Riahc4 have you ever made a skin to say its easy?
Yes Plus! simplifies the resource replacement process, but it can still be tedious when you get to UIFiles.