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an improvement on the principle of parsimony

This needs a catchy name--badly.  Also, maybe this is more accurately called an improvement on methodological naturalism.  But here goes (parsimony is #2 in the following list):
1. Conservation of wonder:  When describing the explanandum, don't make it sound less interesting than it really is.  For example, don't describe a sonnet as a meaningful combination of letters: it's more than that.  
2. Prefer the familiar to the exotic.  When explaining, strive to come up with explanations that rely on analogies with what is more familiar... when doing so is adequate to the task.  In other words, assign the types of properties associated with quarks only as a kind of last resort.
3. Distinguish rather than separate.  Look for how two things are different aspects of the same whole.  As in electo/magnetism. 
4. Identify the limits of the applicability of your analogies:  Every analogy limps if you make it walk far enough. 

This will accomplish as much good as the principle of parsimony / methodological naturalism but without leading to ideological battles.  More interestingly, if human agency is a kind of exemplary cause of the object of knowledge, then science that conforms to these four principles will discover everything that a methodological naturalist would do, while recognizing how the universe has the rational animal as its apex, pointing to Common Good of the Universe.  In other words, this is a kind of methodological naturalism with nature as such pointing to the divine.
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