You know, the more and more I hear this kind of debate (and it's very very often the maple/mahogany one), I'm more tempted to try and build two identical guitars (except for the change you listed) for this very reason. Purely for my own learning, I don't think there's an exact answer, but one of the things that gets me most excited about building guitars is the opportunity to try and test new things. Like how an LP would sound if you used a Wenge cap instead of maple, or making a strat with a bocote neck/ziricote board instead of the usual maple/rosewood or maple/maple.
Luthierie isn't a science, I think it's an art. Yes, some elements require precise dimensions etc, but the constantly varying nature of construction materials (wood), means that you can't analyse it down to percentages. Kind of like cooking, there's no one recipe for a great-tasting dish (or great sounding guitar), but the most fun I have cooking is when I experiment with new ingredients and see what happens. Ok, there may be some times when it doesn't quite taste right, but using my past experience making food, I know what flavours can work together to try and save it by say adding a few herbs. I reckon it can be the same for guitar building, building up experience, and building on tried and true guitar recipes (like the old Maple/Hog body, Hog neck Gibson recipe!). I know that's pretty much repeating Drak and Rich, but figured I'd throw down anyway
Hmm, after my semi-related food comments, I'm hungry...