Nothing, with the exception of tire wear that seems premature. This may be the result of aggressive driving on my part as opposed to any shortcomings of the car... The check engine light comes on occasionally at what seems to be regular service intervals i.e. 20,000,25,000 miles. which is disconcerting, but poses no real problem.
This Cougar is my first car and I have been extremely happy with it. I acquired it with absolutely zero scratches etc, no problems and was clean overall. Likes: Looks (sporty design, interior appearance, etc.) the interior (very sporty; all black with leather wrapped wheel and some faux carbon fiber surfaces), 4 wheel discs with 16' alloys (I am buying some 18" wheels with low profile tires as a purely appearance modification), simplicity and ease of use of HVAC and 6 cd changer (Even after I put in a subwoofer system I kept the stock head unit since it was so good),also, good stock speakers, 5 speed manual, trunk size, sporty handling, good gas mileage (23-26 in suburban driving, 32+ hwy), too many likes to list.
Dislikes:
Tiny backseat, no headroom in back seat, it is hard to get into the backseat (come on it's a coupe) shifter is balky when car is cold, fans on top speed are not uber-strong, black interior makes car very hot when the sun is out, tires not particularly grippy, only 1 practical cupholder in the front and 1 in back, center console is wobbly implying cheapness, wheels collect brake dust quickly, it is not very good in the snow: it does not have ABS or traction control. I would also like a sunroof.
As you can see, my dislikes are very minor and superficial; this car has been great for me and in a year of use and almost 10,000 miles the only thing I have had to do is change the oil, although if I was not getting new rims I would have to replace the tires shortly. I have read horror stories about 99 Cougars; it seems as though I have avoided this curse.
There is/was no Cougar S that ever went into production. There were plans for it and even some promotional materials released -- it was going to have the same 196hp V6 that was in the Ford Contour SVT -- but Ford scrapped their plans at the last second (not sure why).
They scraped the Cougar S because they were worried that it would be too much competition for the Mustang. That is what I have heard.