Design wise, I prefer the front end of the NON S versions, and I wanted to buy aftermarket alloys so that I wouldn't have the same wheels as every other Corolla out there. The cost savings also allow me to buy little extras (bumper guard, door sill enhancements, leather seat covers and aforementioned Alloy wheels with snow tires, etc) without feeling like I'm wasting money.
I chose the L since a manual transmission was a must, and I didn't want to spend more for the S with manual (if I could have even located one). For me, going through the list of upgrades above the L level, either I had them in my previous cars and never used them, or I really didn't care enough about them. (Except for the power door lock remote, which I mistakenly assumed would be included with the power locks on the L when I bought the car)
There are definitely aspects of the S that are better than my car, it's just a case of what matters to people at the time, I think.