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I've owned both..at the same time! I have an 2000S but added a 1998 base car that was an absolute bargain. I enjoyed every minute in the base car but when I would go back to the S, I felt it to be more effortlessly enjoyable.
If I'd been able to afford a new Box back in the day, I would have ended up with a base because I wouldn't have been willing to part with the extra $5-6K for an S. Now, the price difference between the two has narrowed to $1.5-2.5K in my neck of the woods. My buy decision would be based more on the condition and pedigree of the specific car for sale.
As for the 6speed tranny, I added the second gear detent (google for more info) about 4 year ago as occasionally my car would pop out of second gear when box was cold (gear oil had been replaced with P-car gear oil). The detent fixed the issue and I've had no further problems, now at 132K miles.
I don't track my cars so the extras of the S only appeal to me by feel. It certainly doesn't mean I wouldn't buy another base car, given the right circumstances.
Get whichever suits you best, either way you won't be disappointed.
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