I get what you're saying to a degree, pressone, but I also think there are a huge number of things we change about how we look that could equally fit into your categories, but aren't questioned in the way that wearing make up is.
Take your hair, for example. Without meaning to sound as if I am being defensive (I'm not) then would you equally question why someone wanted a haircut, or a hairstyle, rather than leaving their hair to grow as it naturally wants? No one naturally has a fringe, say. I wouldn't imagine the same level of questioning of a woman who wanted to have a fringe because she felt it made her face look better (i.e. suited her face shape).
So in terms of "changing what you look like" to "feel better" - I think most of us do this one way or another an awful lot of the time. You comb, tidy or tie up your hair because you think it looks better. You put on certain clothes because they make you feel better. Make up isn't especially different from that.
Personally I think it's quite a natural human impulse to do or wear things that make you look or feel better. It's certainly not a modern development at all. It does have a correlation with time/money, though, certainly.
Glancing through the replies most people aren't actually wearing a huge amount of make up and it looks as though most people are wearing a combination of primer, foundation, powder and blush which, if the right product, just evens out your colour, and then something on or around their eyes as well.