Well, if stores carried all the exact same sizing, and the exact same fit-then the clothes would only fit about 5% of us.
Men are pretty standard, and mainly it is because they are built pretty much the same. If they carry excess weight, it is usually in their torso mainly (gut/love handles/manboobs/etc.) and their lower bodies usually stay pretty straight up and down. If they find their waist and length, everything pretty much fits them.
Women are different-some of us are hourglass with a defined waist and curvy hios, some are apple shapes with a chubbier waist and no hips...some are A cups and some are DD cups. Because of the differences in womens figure types, plus height differences, it really would be impossible for the pants to run like mens.
For instance-the low rise flare leg jeans that have been in fashion the past few years are wonderful for apple figures. They are low so the waist measurement isn't an issue, and they are slim cut through the hips and thighs-basically modeled after an apple figure. Most curvy hourglasses can't fit into them (myself included!) If I buy them big enough to fit my butt, the waistline is way too big, and they fall down to "plumber crack" level.
My apple friend would prefer Old Navy low rise boot cut, while I preferred Old Navy "Curvy" jeans...fuller through the hips and thighs, and a higher waist that is more defined. They would cut into her waist (too tight) and be baggy in the rear on her.
You just have to find what fit, fits YOU. Women aren't one style fits all, like men are.

One woman who wears a medium might wear a 36B and the next medium a 34C. We are simply too different to be put in men's sizing systems.
My biggest bit of advice is to read the description either online, or if they are on the tag (like at Old Navy) of the fit. They will say low rise/relaxed hips and thighs/slim cut/at the waist/etc. try on the fit that fits your body type more.
For those wearing plus sizes, Lane Bryant just came out with a line of jeans meant for the apple (straight), the regular fit (average curvy), and the curvy (where the waist is much smaller compared to the butt. You can go to their site and put your measurements in, and they will give you your fit "color".