The 98-99 limits you to base only.
I agree with Jager: the comment from your associate makes no sense.
I've owned my 01S for three years and have taken it on two road trips of over 4,000 miles. I did a lot of research before making the purchase, and the main factor for me was the 6-speed in the S vs. the 5-speed in the base for long-distance interstate drives.
The only people who could give you a good response are those who have owned/driven both with similar model years. Car magazines have those people. Here's some research for you.
Porsche Boxster S - First Drive Review - Car Reviews - Car and Driver
Porsche Boxster S - Road Test - Car Reviews - Car and Driver
Search all the C&D reviews for Boxster, and you'll get more information and comparisons to other similar vehicles.
For me, the major differences are lower price and relatively better mpg on the base vs. better acceleration (torque grunt), high-speed cruise "comfort" (these are stiffly sprung sports cars) and braking. But never having driven nor owned a base 986, it's difficult for me to say I wouldn't have just as much fun with it.
DBear