think its down to preference. Ive switched a fairbit between native and 5:4 and 4:3, sometimes I like playing on one rather then the other. I think player models are bigger(everythings kinda bigger) on stretched could be wrong.
I have a 15 inch laptop monitor so 1280x960 makes my crosshair and enemies look bigger so I like it. It's difficult to get used to it at the beginning but once you get used to it you'll love it