With garlic, the more you chop it up, the more flavor you're getting. Think of garlic as having little cells full of garlicky goodness. When you chop up these cells, you get more out of them.
So when you don't peel your garlic, you're just getting the very lightest of flavor from the garlic. I personally luuuurve garlic and try to get the most garlicky I can get out of it but when you only want a slight hint of it, putting them in whole works.