During the five months I have owned my Prelude I have had to replace the entire clutch assembly and shift linkage system.
I had to take the car back to the dealer due to a defective throwout bearing. It was replaced under warranty.
The 2nd and 3rd gear syncros are beginning to go.
The sunroof rattles constantly.
The dashboard has recently begun to rattle as well.
On warm days the back seat dash rubs against the rear window creating yet another rattle.
My previous car, a 1995 civic SI, was a beautiful car. It never gave me problems like these. I understand though that these problems have arisen either due to previous owner neglect or just age itself.
Still, the 5th generation prelude is a great car. I love its performance and its willingness to do what I ask of it. With proper care and routine maintenance, a Honda will last forever.
One last comment. because Preludes are in general a "rare" car, repair costs tend to be more than average.
I own a 2001 Honda Prelude and have had no problems with it (so far). It sounds like you have a lemon and if I were you then I would be very upset with the dealer. I have not heard of anyone having the problems that you descibe. Better luck in the future.
Cheers.