Here is what I've learned. 100% cotton Hakama are probably the most traditional when it comes to fabric; that aside, I'm pretty certain that cotton/polyester blend hakama typically last a little longer. Cotton hakama tend to fade over time and with washings (whether tub-soaked or machine washed), while the cotton/polyester blend hakama hold their color better.
Cotton/polyester blend hakama seem to hold their pleats better, at least this has been my finding. During Iaido practice, you will be moving about on your feet and quite a bit in shikko, you will want a hakama which is durable, a hakama which will stand up to moving about on your knees. The same can be said for Aikido during Suwari Waza and Hanmi Hantachi Waza. My belief is that a cotton/polyester blend will stand up better.
Personally, I've owned several hakama. My first was a cheapy cotton/polyester blend that turned to garbage after about one month (you get what you pay for). My second was a nice Mugendo Budogu Tetron fabric hakama. It has stood the test of time, but I've since turned it over to my wife because it fits her better. My present hakama is a Bu Jin 8 oz. cotton/polyester twill blend. I love it! It holds pleats well, withstands the children tugging on it, and the "knees" have not even begun to show wear. My only recommendation with this hakama is that you either tub-soak it a few times or machine wash it before wearing it; otherwise you will turn your dogi black (or blue, depending on color of hakama).